PCDH19 (Protocadherin-19) variants and mutations
PCDH19 (also known as Protocadherin-19) is a human protein-coding gene encoding a protocadherin-19 protein. It mediates calcium-dependent cell adhesion in developing neural circuits, where mixed populations of variant and normal cells can disrupt network organization. Heterozygous loss-of-function variants classically cause clustering epilepsy in females with variable developmental and behavioral impairment. This analysis covers 1,713 PCDH19 variants and mutations. Of these, 71% have computational variant effect predictions. Disease context includes developmental and epileptic encephalopathy, 9, hereditary disease, and Seizure. Example PCDH19 variants include M1I, S3*, and L4F.
Variant analysis overview
- Gene: PCDH19
- Protein: Protocadherin-19
- UniProt accession: Q8TAB3
- Organism: Homo sapiens
- Variants analyzed: 1713
- Variant scope: all variants
- Completed: 2026-08-19
Variant and mutation evidence
- Variant composition: 1,399 unspecified-consequence records; 3 stop lost; 141 synonymous variants; 152 missense variants; 9 frameshift variants; 2 stop-gained variants; 4 in-frame deletions; 1 splice-region variants; 2 substitution
- Prediction scores: 1,222 variants have prediction scores (71% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: developmental and epileptic encephalopathy, 9, hereditary disease, Seizure, X-linked intellectual disability - epilepsy, Bilateral tonic-clonic seizure, glycine encephalopathy, Dravet syndrome, encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalo, early-infantile DEE, X-linked complex neurodevelopmental disorder, epilepsy, Intellectual disability.
Protein structure and variant hotspots
- Protein features: 1 transmembrane segments; 6 domains; 78 binding sites; 6 post-translational modification sites.
- Structural context: 875 variants have structural context.
- PTM context: 3 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable PCDH19 variants
Examples include M1I, S3*, L4F, L6V, P7L, P7Q, V8M, L9V. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs2147543046, ClinGen CA414011578, ClinVar RCV001379045, MetaLR 0.10, MetaSVM -1.05, Pathogenic, Developmental and epileptic encephalopathy, 9
- S3* (p.Ser3Ter), rs2520999960, ClinGen CA414011564, ClinVar RCV003006136, CADD 35.00, Pathogenic
- L4F (p.Leu4Phe), ExAC rs768501681, REVEL 0.13, CADD 22.30
- L6V (p.Leu6Val), Ensembl rs1928487635
- P7L (p.Pro7Leu), rs1350725154, TOPMed rs1350725154, gnomAD rs1350725154, REVEL 0.07, CADD 18.00, Variant assessed as somatic; moderate impact.
- P7Q (p.Pro7Gln), TOPMed rs1350725154, gnomAD rs1350725154, REVEL 0.08, CADD 15.10
- V8M (p.Val8Met), gnomAD rs1255191262, REVEL 0.12, CADD 15.70
- L9V (p.Leu9Val), 1000Genomes rs746805969
- L11M (p.Leu11Met), ExAC rs775517393, gnomAD rs775517393, REVEL 0.20, CADD 22.80, Likely benign
- A13D (p.Ala13Asp), gnomAD rs1416649514, REVEL 0.18, CADD 18.60
- A13T (p.Ala13Thr), rs1928484938, ClinGen CA414011515, ClinVar RCV003862015, TOPMed rs1928484938, REVEL 0.12, CADD 19.40, Uncertain significance, Developmental and epileptic encephalopathy, 9
- L15M (p.Leu15Met), rs1928483733, ClinGen CA414011502, ClinVar RCV002653307, REVEL 0.11, CADD 15.40, Uncertain significance, Developmental and epileptic encephalopathy, 9
- L15V (p.Leu15Val), Ensembl rs1928483733
- W16C (p.Trp16Cys), ExAC rs780814145, TOPMed rs780814145, gnomAD rs780814145, REVEL 0.22, CADD 23.40, Uncertain significance, not provided
- T17M (p.Thr17Met), rs1928483128, ClinGen CA414011484, cosmic curated COSV55258, ClinVar RCV003134766, REVEL 0.16, CADD 22.60, Uncertain significance, Developmental and epileptic encephalopathy, 9
- Q18* (p.Gln18Ter), rs2147542870, ClinGen CA414011481, ClinVar RCV001972159, ClinVar RCV004571657, CADD 35.00, Pathogenic
- A19V (p.Ala19Val), rs1928482665, ClinGen CA414011470, ClinVar RCV001056266, Ensembl rs1928482665, REVEL 0.11, CADD 22.50, Uncertain significance, Developmental and epileptic encephalopathy, 9
- A20P (p.Ala20Pro), rs1413763025, ClinGen CA414011468, ClinVar RCV000700166, TOPMed rs1413763025, REVEL 0.15, CADD 18.30, Uncertain significance, Developmental and epileptic encephalopathy, 9
- A20T (p.Ala20Thr), TOPMed rs1413763025, gnomAD rs1413763025, REVEL 0.11, CADD 16.70, Uncertain significance, Inborn genetic diseases
- A20V (p.Ala20Val), rs2520999260, ClinGen CA414011465, ClinVar RCV003332735, REVEL 0.14, CADD 18.70, Uncertain significance, not provided
- L22F (p.Leu22Phe), gnomAD rs1159361280
- L25P (p.Leu25Pro), rs2520999081, ClinGen CA414011433, ClinVar RCV003064748, UniProt VAR 067472, REVEL 0.80, CADD 27.90, Pathogenic, Developmental and epileptic encephalopathy, 9
- K26M (p.Lys26Met), rs755403368, ClinGen CA10469018, ClinVar RCV000793687, ClinVar RCV003166107, REVEL 0.54, AlphaMissense 0.73, Uncertain significance, Developmental and epileptic encephalopathy, 9; not provided
- K26Q (p.Lys26Gln), cosmic curated COSV10584, TOPMed rs1323897119, gnomAD rs1323897119, REVEL 0.23, CADD 26.50
- K26R (p.Lys26Arg), ExAC rs755403368, TOPMed rs755403368, gnomAD rs755403368, REVEL 0.30, AlphaMissense 0.73, Uncertain significance
- K26T (p.Lys26Thr), rs755403368, ClinGen CA414011427, ClinVar RCV001752838, ExAC rs755403368, AlphaMissense 0.73, MetaLR 0.21, Uncertain significance, not provided
- Y27* (p.Tyr27Ter), rs56307810, ClinGen CA414011416, ClinVar RCV001092888, 1000Genomes rs56307810, CADD 35.00, Pathogenic
- Y27N (p.Tyr27Asn), rs1928481376, ClinGen CA414011423, ClinVar RCV001348236, Ensembl rs1928481376, AlphaMissense 0.99, MetaLR 0.46, Uncertain significance, Developmental and epileptic encephalopathy, 9
- S28* (p.Ser28Ter), rs766962106, ClinGen CA414011412, ClinVar RCV001775401, ExAC rs766962106, CADD 35.00, Likely pathogenic
- S28A (p.Ser28Ala), rs2520998872, ClinGen CA414011413, ClinVar RCV002671261, Uncertain significance, Developmental and epileptic encephalopathy, 9
- S28W (p.Ser28Trp), ExAC rs766962106, gnomAD rs766962106, REVEL 0.46, CADD 26.00, Likely pathogenic
- V29L (p.Val29Leu), gnomAD rs1270264066, REVEL 0.23, CADD 22.50
- E30K (p.Glu30Lys), rs931969825, ClinGen CA333826111, ClinVar RCV001876331, ClinVar RCV004953164, REVEL 0.10, CADD 22.70, Uncertain significance, Inborn genetic diseases; Developmental and epileptic encephalopathy, 9
- E31* (p.Glu31Ter), rs796052794, ClinGen CA316278, ClinVar RCV000188342, Ensembl rs796052794, AlphaMissense 0.99, MetaLR 0.54, Pathogenic
- E31K (p.Glu31Lys), rs796052794, ClinGen CA414011397, ClinVar RCV000700933, Ensembl rs796052794, AlphaMissense 0.99, MetaLR 0.54, Pathogenic, Developmental and epileptic encephalopathy, 9
- E31V (p.Glu31Val), rs1064795834, ClinGen CA16621152, ClinVar RCV000485018, Ensembl rs1064795834, AlphaMissense 1.00, MetaLR 0.52, Likely pathogenic, not provided
- E32V (p.Glu32Val), rs2147542709, ClinGen CA414011386, ClinVar RCV001822990, Ensembl rs2147542709, AlphaMissense 0.98, MetaLR 0.51, Likely pathogenic, PCDH19-related epilespy
- Q33* (p.Gln33Ter), rs1928479952, ClinGen CA414011381, cosmic curated COSV55261, ClinVar RCV002274362, CADD 35.00, Pathogenic
- Q33E (p.Gln33Glu), TOPMed rs1928479952, Pathogenic
- Q33H (p.Gln33His), NCI-TCGA Cosmic COSV9972, cosmic curated COSV99720, Ensembl rs1928479672, Variant assessed as somatic; moderate impact.
- Q33K (p.Gln33Lys), rs1928479952, ClinGen CA414011383, ClinVar RCV003228488, REVEL 0.12, CADD 17.20, Uncertain significance, not provided
- Q33R (p.Gln33Arg), gnomAD rs1229227215, REVEL 0.15, CADD 20.10
- A35P (p.Ala35Pro), rs2147542686, ClinGen CA414011368, ClinVar RCV002048545, Ensembl rs2147542686, AlphaMissense 0.18, MetaLR 0.04, Uncertain significance, Developmental and epileptic encephalopathy, 9
- A35T (p.Ala35Thr), NCI-TCGA Cosmic COSV5526, cosmic curated COSV55262, REVEL 0.11, CADD 23.60, Variant assessed as somatic; moderate impact.
- A35V (p.Ala35Val), gnomAD rs1328655427, REVEL 0.13, CADD 24.40
- G36R (p.Gly36Arg), rs1928479255, ClinGen CA414011362, ClinVar RCV003076900, ClinVar RCV003229931, REVEL 0.62, CADD 26.20, Uncertain significance, Developmental and epileptic encephalopathy, 9; not provided
- I39L (p.Ile39Leu), rs2520998383, ClinGen CA414011345, ClinVar RCV003039823, Uncertain significance, Developmental and epileptic encephalopathy, 9
- N41D (p.Asn41Asp), 1000Genomes rs1341619338, gnomAD rs1341619338, REVEL 0.11, CADD 23.10
- N41K (p.Asn41Lys), TOPMed rs1928478516, REVEL 0.30, CADD 22.60
- N41S (p.Asn41Ser), rs2147542647, ClinGen CA414011328, ClinVar RCV002028165, Ensembl rs2147542647, REVEL 0.26, CADD 23.80, Uncertain significance, Developmental and epileptic encephalopathy, 9
- V42L (p.Val42Leu), ExAC rs767840869, gnomAD rs767840869, REVEL 0.15, AlphaMissense 0.82, Uncertain significance
- V42M (p.Val42Met), rs767840869, ClinGen CA414011324, cosmic curated COSV10808, ClinVar RCV001771308, AlphaMissense 0.82, MetaLR 0.19, Uncertain significance, not provided; Developmental and epileptic encephalopathy, 9
- A43T (p.Ala43Thr), NCI-TCGA Cosmic COSV5526, cosmic curated COSV55262, REVEL 0.12, CADD 21.60, Variant assessed as somatic; moderate impact.
- A43V (p.Ala43Val), rs1064795511, ClinGen CA16621151, ClinVar RCV000478041, TOPMed rs1064795511, REVEL 0.23, CADD 23.60, Likely pathogenic, not provided
- A46V (p.Ala46Val), cosmic curated COSV10454, gnomAD rs1391222418, REVEL 0.26, CADD 24.00
- R47* (p.Arg47Ter), rs762069884, ClinGen CA414011292, ClinVar RCV003384296, AlphaMissense 0.19, MetaLR 0.04, Pathogenic
- R47G (p.Arg47Gly), ExAC rs762069884, gnomAD rs762069884, REVEL 0.16, AlphaMissense 0.19
- R47L (p.Arg47Leu), rs2520998053, ClinGen CA414011289, ClinVar RCV003037537, REVEL 0.05, CADD 18.50, Uncertain significance, Developmental and epileptic encephalopathy, 9
- R47Q (p.Arg47Gln), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- E48* (p.Glu48Ter), rs132630326, ClinGen CA121300, ClinVar RCV000011767, gnomAD rs132630326, AlphaMissense 0.22, MetaLR 0.07, Pathogenic
- E48G (p.Glu48Gly), Ensembl rs1928477025
- E48K (p.Glu48Lys), gnomAD rs132630326, Pathogenic
- A49T (p.Ala49Thr), rs1405217506, ClinGen CA414011281, NCI-TCGA Cosmic COSV5526, cosmic curated COSV55260, REVEL 0.07, CADD 23.10, Uncertain significance, Developmental and epileptic encephalopathy, 9
- A49V (p.Ala49Val), NCI-TCGA TCGA novel, REVEL 0.12, CADD 23.40, Variant assessed as somatic; moderate impact.
- A52P (p.Ala52Pro), rs1928476742, ClinGen CA414011261, ClinVar RCV003328031, ClinVar RCV003509807, REVEL 0.12, CADD 22.60, Uncertain significance, not provided; Developmental and epileptic encephalopathy, 9
- A52T (p.Ala52Thr), NCI-TCGA TCGA novel, REVEL 0.03, CADD 17.90, Variant assessed as somatic; moderate impact.
- A52V (p.Ala52Val), rs2147542586, ClinGen CA414011258, NCI-TCGA Cosmic COSV9972, cosmic curated COSV99720, AlphaMissense 0.07, MetaLR 0.04, Uncertain significance, Developmental and epileptic encephalopathy, 9
- D54E (p.Asp54Glu), NCI-TCGA TCGA novel, REVEL 0.09, CADD 15.10, Variant assessed as somatic; moderate impact.
- D54G (p.Asp54Gly), NCI-TCGA Cosmic COSV5525, NCI-TCGA Cosmic COSV9971, cosmic curated COSV99718, Variant assessed as somatic; moderate impact.
- P55A (p.Pro55Ala), ExAC rs774662487, TOPMed rs774662487, gnomAD rs774662487, REVEL 0.02, CADD 5.97, Likely benign
- P55R (p.Pro55Arg), rs1928476240, ClinGen CA414011239, ClinVar RCV001229588, Ensembl rs1928476240, AlphaMissense 0.14, MetaLR 0.06, Uncertain significance, Developmental and epileptic encephalopathy, 9
- P55S (p.Pro55Ser), rs774662487, ClinGen CA414011242, ClinVar RCV002301956, ClinVar RCV002400431, REVEL 0.02, CADD 8.38, Conflicting interpretations, Inborn genetic diseases; not provided; Developmental and epileptic encephalopath
- R56G (p.Arg56Gly), rs940541141, ClinGen CA333826109, ClinVar RCV003621927, ClinVar RCV004721210, REVEL 0.17, CADD 21.10, Uncertain significance, not provided; Developmental and epileptic encephalopathy, 9
- R56L (p.Arg56Leu), NCI-TCGA Cosmic COSV9972, cosmic curated COSV99720, Variant assessed as somatic; moderate impact.
- R56Q (p.Arg56Gln), rs1928475827, ClinGen CA414011236, ClinVar RCV001982385, TOPMed rs1928475827, REVEL 0.06, CADD 19.50, Uncertain significance, Developmental and epileptic encephalopathy, 9
- Q57* (p.Gln57Ter), rs1367823627, ClinGen CA414011231, ClinVar RCV000516328, ClinVar RCV005091194, CADD 35.00, Pathogenic
- Q57R (p.Gln57Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- A58S (p.Ala58Ser), rs763745318, ClinGen CA10469011, ClinVar RCV001217909, ClinVar RCV005257999, REVEL 0.05, CADD 16.30, Uncertain significance, Developmental and epileptic encephalopathy, 9; Inborn genetic diseases
- A60S (p.Ala60Ser), gnomAD rs1303036388, REVEL 0.08, CADD 15.10
- A60V (p.Ala60Val), ExAC rs762855456, gnomAD rs762855456, REVEL 0.10, CADD 18.70
- R62C (p.Arg62Cys), NCI-TCGA Cosmic COSV5526, cosmic curated COSV55265, Variant assessed as somatic; moderate impact.
- R62H (p.Arg62His), cosmic curated COSV55260, ExAC rs775259534, gnomAD rs775259534
- R62L (p.Arg62Leu), ExAC rs775259534, gnomAD rs775259534, REVEL 0.60, CADD 24.90
- S65F (p.Ser65Phe), rs769833284, ClinGen CA10469008, ClinVar RCV001752392, ExAC rs769833284, REVEL 0.44, CADD 26.40, Uncertain significance, not provided
- N66S (p.Asn66Ser), rs1357065341, ClinGen CA414011176, ClinVar RCV003047402, gnomAD rs1357065341, REVEL 0.17, CADD 23.50, Uncertain significance, Developmental and epileptic encephalopathy, 9
- S67* (p.Ser67Ter), rs868762744, ClinGen CA414011169, ClinVar RCV001092887, ClinVar RCV005093464, AlphaMissense 0.75, MetaLR 0.24, Pathogenic
- S67L (p.Ser67Leu), cosmic curated COSV99719, Ensembl rs868762744, Pathogenic
- S67W (p.Ser67Trp), rs868762744, ClinGen CA414011168, ClinVar RCV002275666, Ensembl rs868762744, AlphaMissense 0.75, MetaLR 0.24, Uncertain significance, Developmental and epileptic encephalopathy, 9
- A68D (p.Ala68Asp), TOPMed rs1928473737, gnomAD rs1928473737, REVEL 0.09, AlphaMissense 0.46, Uncertain significance
- A68T (p.Ala68Thr), rs1064797379, ClinGen CA16621904, ClinVar RCV000488326, ClinVar RCV001054798, REVEL 0.13, CADD 23.30, Uncertain significance, not provided; Developmental and epileptic encephalopathy, 9
- A68V (p.Ala68Val), rs1928473737, ClinGen CA414011163, ClinVar RCV001973733, TOPMed rs1928473737, AlphaMissense 0.46, MetaLR 0.16, Uncertain significance, Developmental and epileptic encephalopathy, 9
- P69A (p.Pro69Ala), TOPMed rs1457943470, REVEL 0.10, CADD 24.40
- H70L (p.His70Leu), TOPMed rs1602638349, REVEL 0.13, CADD 22.30
- L71I (p.Leu71Ile), rs2520997105, ClinGen CA414011148, ClinVar RCV003622701, Uncertain significance, Developmental and epileptic encephalopathy, 9
- V72A (p.Val72Ala), ExAC rs776058393, gnomAD rs776058393, REVEL 0.37, CADD 26.80, Uncertain significance, Developmental and epileptic encephalopathy, 9
- V72G (p.Val72Gly), UniProt VAR 067473, Conflicting interpretations, not provided; Developmental and epileptic encephalopathy, 9
- V72L (p.Val72Leu), Ensembl rs1928473088
- D73E (p.Asp73Glu), rs1928472700, ClinGen CA414011131, ClinVar RCV001199410, Ensembl rs1928472700, AlphaMissense 0.34, MetaLR 0.04, Uncertain significance, Periventricular nodular heterotopia and epilepsy
- D73G (p.Asp73Gly), rs2520997042, ClinVar RCV004577174, Uncertain significance, Developmental and epileptic encephalopathy, 9
- I74M (p.Ile74Met), rs1064797378, ClinGen CA16621903, ClinVar RCV000487980, gnomAD rs1064797378, AlphaMissense 0.47, MetaLR 0.21, Uncertain significance, not provided
- N75S (p.Asn75Ser), rs796052790, ClinGen CA316233, ClinVar RCV000188327, ClinVar RCV000764882, REVEL 0.10, CADD 20.50, Uncertain significance, not specified; Developmental and epileptic encephalopathy, 9; not provided
- P76L (p.Pro76Leu), cosmic curated COSV55269, Ensembl rs866570451
- P76S (p.Pro76Ser), TOPMed rs1433970971, gnomAD rs1433970971, REVEL 0.07, CADD 23.00, Uncertain significance, Developmental and epileptic encephalopathy, 9
- L80Q (p.Leu80Gln), gnomAD rs1405458717, REVEL 0.20, CADD 26.20
- L80V (p.Leu80Val), ExAC rs770435361, gnomAD rs770435361, REVEL 0.02, CADD 10.30
- L81R (p.Leu81Arg), rs1569316056, ClinGen CA414011078, ClinVar RCV000698231, UniProt VAR 064840, AlphaMissense 1.00, MetaLR 0.47, Pathogenic, Developmental and epileptic encephalopathy, 9
- V82A (p.Val82Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V82I (p.Val82Ile), cosmic curated COSV10504, TOPMed rs1389369756, gnomAD rs1389369756, REVEL 0.03, CADD 18.50
- T83I (p.Thr83Ile), gnomAD rs1161661796, REVEL 0.28, CADD 26.10
- Q85* (p.Gln85Ter), rs132630324, ClinGen CA121295, ClinVar RCV000011764, Ensembl rs132630324, Pathogenic
- Q85R (p.Gln85Arg), rs1928470713, ClinGen CA414011014, ClinVar RCV001227636, Ensembl rs1928470713, AlphaMissense 0.48, MetaLR 0.10, Uncertain significance, Developmental and epileptic encephalopathy, 9
- K86* (p.Lys86Ter), rs2520996511, ClinGen CA414011001, ClinVar RCV003013335, Pathogenic
- K86N (p.Lys86Asn), TOPMed rs1928470554
- I87F (p.Ile87Phe), NCI-TCGA Cosmic COSV9971, cosmic curated COSV99719, Variant assessed as somatic; moderate impact.
- D90G (p.Asp90Gly), rs2147542320, ClinGen CA414010933, ClinVar RCV002000444, Ensembl rs2147542320, AlphaMissense 0.99, MetaLR 0.17, Likely pathogenic, Developmental and epileptic encephalopathy, 9
- D90H (p.Asp90His), rs1555985780, ClinGen CA414010941, ClinVar RCV000529603, Ensembl rs1555985780, AlphaMissense 0.99, MetaLR 0.20, Likely pathogenic, Developmental and epileptic encephalopathy, 9
- L91M (p.Leu91Met), ExAC rs746627230, TOPMed rs746627230, gnomAD rs746627230, REVEL 0.01, CADD 14.70
- R94H (p.Arg94His), ESP rs377309648, ExAC rs377309648, gnomAD rs377309648
- Q95R (p.Gln95Arg), ExAC rs755279531
- P97L (p.Pro97Leu), rs2520996278, ClinGen CA414010833, ClinVar RCV003623681, REVEL 0.33, CADD 24.30, Uncertain significance, Developmental and epileptic encephalopathy, 9
- K98Q (p.Lys98Gln), rs372702479, ClinGen CA333826103, ClinVar RCV001947706, ESP rs372702479, REVEL 0.12, CADD 22.40, Uncertain significance, Developmental and epileptic encephalopathy, 9; Inborn genetic diseases
- K98R (p.Lys98Arg), rs1240585527, NCI-TCGA Cosmic COSV5527, cosmic curated COSV55272, gnomAD rs1240585527, REVEL 0.17, CADD 25.40, Variant assessed as somatic; moderate impact.
- C99S (p.Cys99Ser), rs1064795237, ClinGen CA16621150, ClinVar RCV000485618, Ensembl rs1064795237, AlphaMissense 1.00, MetaLR 0.43, Uncertain significance, Developmental and epileptic encephalopathy, 9
- C99Y (p.Cys99Tyr), rs2147542235, ClinGen CA414010805, ClinVar RCV001784157, ClinVar RCV004719174, AlphaMissense 1.00, MetaLR 0.45, Conflicting interpretations, Developmental and epileptic encephalopathy, 9; not provided
- I100F (p.Ile100Phe), rs796052838, ClinGen CA316415, ClinVar RCV000188400, ClinVar RCV001857630, REVEL 0.11, CADD 21.30, Uncertain significance, not provided; Developmental and epileptic encephalopathy, 9
- I101V (p.Ile101Val), rs779017688, ClinGen CA238705, ClinVar RCV000724033, ClinVar RCV001301985, REVEL 0.12, CADD 20.60, Uncertain significance, Inborn genetic diseases; Developmental and epileptic encephalopathy, 9; not prov
- S102L (p.Ser102Leu), NCI-TCGA Cosmic COSV5526, cosmic curated COSV55261, Variant assessed as somatic; moderate impact.
- E104K (p.Glu104Lys), NCI-TCGA Cosmic COSV5526, cosmic curated COSV55265, Variant assessed as somatic; moderate impact.
- V105I (p.Val105Ile), ExAC rs756745115, REVEL 0.23, CADD 25.00
- M106I (p.Met106Ile), ExAC rs750982847, REVEL 0.27, CADD 22.60
- M106K (p.Met106Lys), rs2520995882, ClinGen CA414010708, ClinVar RCV002291240, Likely pathogenic, Developmental and epileptic encephalopathy, 9
- M106V (p.Met106Val), ESP rs368355788, TOPMed rs368355788, Uncertain significance, not provided
- S107F (p.Ser107Phe), TOPMed rs1285810900, REVEL 0.26, CADD 27.10
- S108N (p.Ser108Asn), gnomAD rs1298928467, REVEL 0.08, CADD 16.50
- S109T (p.Ser109Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- M110I (p.Met110Ile), rs2520995713, ClinGen CA414010602, ClinVar RCV003623280, Uncertain significance, Developmental and epileptic encephalopathy, 9
- M110V (p.Met110Val), rs1057520139, ClinGen CA16603275, ClinVar RCV000438972, ClinVar RCV005090699, REVEL 0.10, CADD 20.20, Uncertain significance, Developmental and epileptic encephalopathy, 9; not provided
- I112N (p.Ile112Asn), rs2147542128, ClinGen CA414010553, ClinVar RCV001837133, Ensembl rs2147542128, AlphaMissense 0.98, MetaLR 0.26, Uncertain significance, not provided
- I112S (p.Ile112Ser), rs2147542128, ClinGen CA414010547, ClinVar RCV001902448, Ensembl rs2147542128, AlphaMissense 0.98, MetaLR 0.26, Uncertain significance, Developmental and epileptic encephalopathy, 9
- C113W (p.Cys113Trp), ExAC rs757433043, gnomAD rs757433043, Likely benign
- V114A (p.Val114Ala), TOPMed rs1928464556, REVEL 0.22, CADD 21.90
- V114L (p.Val114Leu), ExAC rs751708323, gnomAD rs751708323, REVEL 0.10, CADD 19.50, Uncertain significance, Developmental and epileptic encephalopathy, 9
- V114M (p.Val114Met), rs751708323, ClinGen CA414010513, ClinVar RCV003273248, ClinVar RCV006472180, REVEL 0.12, CADD 23.10, Uncertain significance, Inborn genetic diseases; Developmental and epileptic encephalopathy, 9
- I115K (p.Ile115Lys), rs1928464417, ClinGen CA414010483, ClinVar RCV001210680, Ensembl rs1928464417, AlphaMissense 1.00, MetaLR 0.35, Uncertain significance, Developmental and epileptic encephalopathy, 9
- I119F (p.Ile119Phe), gnomAD rs1928464114, REVEL 0.57, CADD 24.90
- K120N (p.Lys120Asn), rs1214373921, ClinGen CA414010345, ClinVar RCV002587010, ClinGen CA414010347, AlphaMissense 0.62, MetaLR 0.09, Uncertain significance, Developmental and epileptic encephalopathy, 9
- D121A (p.Asp121Ala), rs1928463633, ClinGen CA414010327, ClinVar RCV001233479, Ensembl rs1928463633, AlphaMissense 1.00, MetaLR 0.69, Pathogenic, Developmental and epileptic encephalopathy, 9
- D121H (p.Asp121His), rs796052795, ClinGen CA316284, ClinVar RCV000188345, Ensembl rs796052795, AlphaMissense 1.00, MetaLR 0.77, Likely pathogenic, not provided
- D121N (p.Asp121Asn), rs796052795, ClinGen CA414010340, ClinVar RCV000489751, ClinVar RCV006463059, AlphaMissense 1.00, MetaLR 0.77, Likely pathogenic, Developmental and epileptic encephalopathy, 9; not provided
- N123K (p.Asn123Lys), rs796052796, ClinGen CA316287, ClinVar RCV000188346, ClinVar RCV003621514, AlphaMissense 1.00, MetaLR 0.63, Pathogenic/Likely pathogenic, not provided; Developmental and epileptic encephalopathy, 9; Seizure
- D124A (p.Asp124Ala), rs2147542056, ClinGen CA414010270, ClinVar RCV001378907, Ensembl rs2147542056, AlphaMissense 1.00, MetaLR 0.51, Likely pathogenic, Developmental and epileptic encephalopathy, 9
- D124H (p.Asp124His), rs796052797, ClinGen CA414010276, ClinVar RCV001213098, ClinVar RCV001819902, AlphaMissense 1.00, MetaLR 0.53, Pathogenic, not provided; Developmental and epileptic encephalopathy, 9
- D124N (p.Asp124Asn), NCI-TCGA Cosmic COSV5526, Variant assessed as somatic; moderate impact.
- D124Y (p.Asp124Tyr), rs796052797, ClinGen CA316290, cosmic curated COSV55263, ClinVar RCV000188347, AlphaMissense 1.00, MetaLR 0.53, Likely pathogenic, not provided
- N125S (p.Asn125Ser), rs398123603, ClinGen CA221632, ClinVar RCV000079608, ClinVar RCV001064429, AlphaMissense 0.60, MetaLR 0.28, Pathogenic
- P127L (p.Pro127Leu), rs2147542030, ClinGen CA414010191, ClinVar RCV001985960, Ensembl rs2147542030, AlphaMissense 0.99, MetaLR 0.71, Uncertain significance, Developmental and epileptic encephalopathy, 9
- P127S (p.Pro127Ser), rs1928462873, ClinGen CA414010199, ClinVar RCV001071976, ClinVar RCV002512137, AlphaMissense 1.00, MetaLR 0.71, Pathogenic/Likely pathogenic, not provided; Developmental and epileptic encephalopathy, 9
- S128G (p.Ser128Gly), rs762647337, NCI-TCGA Cosmic COSV5526, cosmic curated COSV55263, ExAC rs762647337, AlphaMissense 0.12, MetaLR 0.08, Variant assessed as somatic; moderate impact.
- F129L (p.Phe129Leu), rs1238011122, ClinGen CA414010077, ClinVar RCV000584834, TOPMed rs1238011122, AlphaMissense 1.00, MetaLR 0.28, Uncertain significance, Developmental and epileptic encephalopathy, 9
- F129S (p.Phe129Ser), rs1602638047, ClinGen CA414010141, ClinVar RCV000810075, Ensembl rs1602638047, AlphaMissense 1.00, MetaLR 0.33, Uncertain significance, Developmental and epileptic encephalopathy, 9
- A132E (p.Ala132Glu), NCI-TCGA Cosmic COSV5526, cosmic curated COSV55260, Variant assessed as somatic; moderate impact.
- I134M (p.Ile134Met), rs41300169, ClinGen CA333826099, ClinVar RCV003112610, 1000Genomes rs41300169, REVEL 0.10, CADD 3.66, Uncertain significance, Developmental and epileptic encephalopathy, 9
- E135* (p.Glu135Ter), rs759398718, ClinGen CA414009854, ClinVar RCV001233401, ExAC rs759398718, AlphaMissense 0.24, MetaLR 0.04, Pathogenic
- E135K (p.Glu135Lys), ExAC rs759398718, gnomAD rs759398718, REVEL 0.13, AlphaMissense 0.24, Pathogenic
- E135Q (p.Glu135Gln), ExAC rs759398718, gnomAD rs759398718, REVEL 0.11, AlphaMissense 0.24, Pathogenic
- E137* (p.Glu137Ter), rs1555985689, ClinGen CA414009827, ClinVar RCV000497495, ClinVar RCV001865562, Pathogenic
- I138N (p.Ile138Asn), rs1602637994, ClinGen CA414009809, ClinVar RCV000809475, Ensembl rs1602637994, AlphaMissense 0.99, MetaLR 0.49, Uncertain significance, Developmental and epileptic encephalopathy, 9
- S139L (p.Ser139Leu), rs1555985687, ClinGen CA414009791, ClinVar RCV000521658, ClinVar RCV001206419, AlphaMissense 0.44, MetaLR 0.31, Conflicting interpretations, not provided; Developmental and epileptic encephalopathy, 9
- E140G (p.Glu140Gly), rs1928460473, ClinGen CA414009780, ClinVar RCV001066474, Ensembl rs1928460473, AlphaMissense 0.99, MetaLR 0.77, Likely pathogenic, Developmental and epileptic encephalopathy, 9
- E140K (p.Glu140Lys), rs2520994737, ClinGen CA414009784, ClinVar RCV003622884, Pathogenic, Developmental and epileptic encephalopathy, 9
- E140Q (p.Glu140Gln), rs2520994737, ClinGen CA414009787, ClinVar RCV003622513, Uncertain significance, Developmental and epileptic encephalopathy, 9
- A141T (p.Ala141Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact., in DEE9
- A142P (p.Ala142Pro), rs796052798, ClinGen CA316293, ClinVar RCV000188348, Ensembl rs796052798, AlphaMissense 0.98, MetaLR 0.46, Likely pathogenic, not provided
- S143C (p.Ser143Cys), NCI-TCGA Cosmic COSV9971, cosmic curated COSV99719, Variant assessed as somatic; moderate impact.
- S143I (p.Ser143Ile), NCI-TCGA Cosmic COSV5527, cosmic curated COSV55272, Variant assessed as somatic; moderate impact.
- S143R (p.Ser143Arg), TOPMed rs1416853682
- P144H (p.Pro144His), rs2520994653, ClinGen CA414009724, ClinVar RCV004505076, Uncertain significance, Inborn genetic diseases
- T146K (p.Thr146Lys), rs796052799, ClinGen CA414009704, ClinVar RCV001211167, Ensembl rs796052799, AlphaMissense 0.74, MetaLR 0.40, Uncertain significance, Developmental and epileptic encephalopathy, 9
- T146M (p.Thr146Met), rs796052799, ClinGen CA414009702, ClinVar RCV003828537, NCI-TCGA Cosmic COSV5526, REVEL 0.61, AlphaMissense 0.74, Likely pathogenic, Developmental and epileptic encephalopathy, 9
- T146R (p.Thr146Arg), rs796052799, ClinGen CA316296, ClinVar RCV000188349, ClinVar RCV001378123, AlphaMissense 0.74, MetaLR 0.40, Likely pathogenic, Developmental and epileptic encephalopathy, 9; not provided
Public PCDH19 analysis runs
- PCDH19 analysis run — PCDH19 (1,713 variants) — completed 2026-08-19