STXBP1 (Syntaxin-binding protein 1) variants and mutations
STXBP1 (also known as Syntaxin-binding protein 1) is a human protein-coding gene encoding a syntaxin-binding protein 1 protein. It controls SNARE-complex assembly and synaptic-vesicle fusion, making it essential for rapid neurotransmitter release. Haploinsufficiency causes STXBP1-related neurodevelopmental disorder with developmental impairment, epilepsy, movement abnormalities, and intellectual disability. This analysis covers 823 STXBP1 variants and mutations. Of these, 64% have computational variant effect predictions. Disease context includes developmental and epileptic encephalopathy, 4, early-infantile DEE, and genetic developmental and epileptic encephalopathy. Example STXBP1 variants include M1K, M1R, and A2T.
Variant analysis overview
- Gene: STXBP1
- Protein: Syntaxin-binding protein 1
- UniProt accession: P61764
- Organism: Homo sapiens
- Variants analyzed: 823
- Variant scope: all variants
- Completed: 2026-08-18
Variant and mutation evidence
- Variant composition: 735 unspecified-consequence records; 5 frameshift variants; 41 missense variants; 24 synonymous variants; 1 stop-gained variants; 2 splice-region variants; 1 in-frame deletions; 3 stop lost; 9 substitution
- Prediction scores: 530 variants have prediction scores (64% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: developmental and epileptic encephalopathy, 4, early-infantile DEE, genetic developmental and epileptic encephalopathy, Intellectual disability, hereditary disease, developmental and epileptic encephalopathy, infantile epilepsy syndrome, Epileptic encephalopathy, Seizure, Global developmental delay, infantile spasms, neurodegenerative disease.
Protein structure and variant hotspots
- Protein features: 5 post-translational modification sites.
- PTM context: 5 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, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable STXBP1 variants
Examples include M1K, M1R, A2T, A2V, A2S, A2P, A2D, A2A. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1K (p.Met1Lys), rs2539639191, ClinGen CA375173528, ClinVar RCV003138849, Uncertain significance, not provided; Early-infantile DEE
- M1R (p.Met1Arg), rs2539639191, ClinGen CA375173530, ClinVar RCV004794596, ClinVar RCV006559933, Pathogenic/Likely pathogenic, Early-infantile DEE; Developmental and epileptic encephalopathy, 4
- A2T (p.Ala2Thr), cosmic curated COSV10890, REVEL 0.19, CADD 25.20
- A2V (p.Ala2Val), rs1838427784, ClinGen CA375173539, ClinVar RCV006466249, Ensembl rs1838427784, AlphaMissense 0.74, MetaLR 0.43, Uncertain significance, Early-infantile DEE
- A2S (p.Ala2Ser), gnomAD 9-127612407-G-T, REVEL 0.07, CADD 22.40
- A2P (p.Ala2Pro), gnomAD 9-127612407-G-C, REVEL 0.28, CADD 25.90
- A2D (p.Ala2Asp), gnomAD 9-127612408-C-A, REVEL 0.27, CADD 24.90
- A2A (p.Ala2Ala), rs144094037, gnomAD 9-127612409-C-T, CADD 14.70
- P3H (p.Pro3His), 1000Genomes rs575515332, ExAC rs575515332, TOPMed rs575515332, gnomAD rs575515332, REVEL 0.34, AlphaMissense 0.48, Uncertain significance
- P3L (p.Pro3Leu), rs575515332, ClinGen CA375173544, ClinVar RCV006561961, 1000Genomes rs575515332, AlphaMissense 0.48, MetaLR 0.46, Uncertain significance, Early-infantile DEE
- P3R (p.Pro3Arg), 1000Genomes rs575515332, ExAC rs575515332, TOPMed rs575515332, gnomAD rs575515332, Uncertain significance
- P3T (p.Pro3Thr), gnomAD 9-127612410-C-A, REVEL 0.26, CADD 22.80
- P3P (p.Pro3Pro), gnomAD 9-127612412-C-G, CADD 15.20
- P3S (p.Pro3Ser), rs968935473, gnomAD 9-127613292-C-T, CADD 15.40
- I4T (p.Ile4Thr), ExAC rs780924917, TOPMed rs780924917, gnomAD rs780924917, REVEL 0.11, CADD 21.30, Uncertain significance, Early-infantile DEE
- I4V (p.Ile4Val), rs2539639296, ClinGen CA375173545, ClinVar RCV003138850, REVEL 0.05, CADD 19.30, Uncertain significance, Developmental and epileptic encephalopathy, 4
- I4H (p.Ile4His), rs1341210726, gnomAD 9-127612407-G-GC, CADD 25.00
- I4L (p.Ile4Leu), gnomAD 9-127612407-GC-G, CADD 24.10
- G5C (p.Gly5Cys), rs1322735925, ClinGen CA375173553, ClinVar RCV006558865, TOPMed rs1322735925, REVEL 0.51, CADD 27.80, Uncertain significance, Early-infantile DEE
- G5S (p.Gly5Ser), gnomAD 9-127612416-G-A, REVEL 0.18, CADD 22.90
- G5R (p.Gly5Arg), gnomAD 9-127612416-G-C, REVEL 0.61, CADD 25.90
- G5V (p.Gly5Val), gnomAD 9-127612417-G-T, REVEL 0.60, CADD 25.00
- G5D (p.Gly5Asp), gnomAD 9-127612417-G-A, REVEL 0.56, CADD 24.70
- G5G (p.Gly5Gly), gnomAD 9-127612418-C-A, CADD 13.40
- L6P (p.Leu6Pro), rs2539639339, ClinGen CA375173562, ClinVar RCV003229392, REVEL 0.67, CADD 26.60, Likely pathogenic, not provided
- L6I (p.Leu6Ile), gnomAD 9-127612419-C-A, REVEL 0.58, CADD 24.10
- L6H (p.Leu6His), gnomAD 9-127612420-T-A, REVEL 0.53, CADD 25.50
- L6L (p.Leu6Leu), rs1209862330, gnomAD 9-127612421-C-G, CADD 13.80
- p.Leu16 Ile17del, gnomAD 9-127613273-ACTTA, CADD 14.30
- K7E (p.Lys7Glu), rs2132275587, ClinGen CA375173564, ClinVar RCV005624496, ClinVar RCV006468289, AlphaMissense 0.97, MetaLR 0.58, Conflicting interpretations, Early-infantile DEE; Seizure
- K7R (p.Lys7Arg), gnomAD 9-127612423-A-G, REVEL 0.44, CADD 24.00
- A8G (p.Ala8Gly), rs1838429772, ClinGen CA375173575, ClinVar RCV001270898, Ensembl rs1838429772, AlphaMissense 0.24, MetaLR 0.35, Uncertain significance, STXBP1-related neurodevelopmental disorder
- A8V (p.Ala8Val), NCI-TCGA Cosmic COSV1009, cosmic curated COSV10096, REVEL 0.33, CADD 22.70, Variant assessed as somatic; moderate impact.
- A8S (p.Ala8Ser), gnomAD 9-127612425-G-T, REVEL 0.23, CADD 22.10
- A8T (p.Ala8Thr), gnomAD 9-127612425-G-A, REVEL 0.26, CADD 22.80
- A8D (p.Ala8Asp), gnomAD 9-127612426-C-A, REVEL 0.49, CADD 23.20
- A8A (p.Ala8Ala), gnomAD 9-127612427-T-C, CADD 15.40
- V9I (p.Val9Ile), rs1262952349, ClinGen CA375173577, ClinVar RCV006609596, gnomAD rs1262952349, REVEL 0.20, CADD 18.80, Benign, Early-infantile DEE
- V9F (p.Val9Phe), gnomAD 9-127612428-G-T, REVEL 0.51, CADD 23.70
- V9D (p.Val9Asp), gnomAD 9-127612429-T-A, REVEL 0.57, CADD 23.90
- V9V (p.Val9Val), rs1838430141, gnomAD 9-127612430-T-G, CADD 15.00
- V10D (p.Val10Asp), rs1838430536, ClinGen CA375173586, ClinVar RCV001090603, Ensembl rs1838430536, AlphaMissense 0.99, MetaLR 0.57, Uncertain significance, not provided
- V10F (p.Val10Phe), gnomAD 9-127612431-G-T, REVEL 0.65, CADD 25.30
- V10I (p.Val10Ile), gnomAD 9-127612431-G-A, REVEL 0.34, CADD 23.00
- V10A (p.Val10Ala), gnomAD 9-127612432-T-C, REVEL 0.48, CADD 23.40
- V10V (p.Val10Val), rs372842480, gnomAD 9-127612433-C-G, CADD 15.40
- G11E (p.Gly11Glu), Ensembl rs1838430719
- G11R (p.Gly11Arg), gnomAD 9-127612434-G-A, REVEL 0.45, CADD 26.50
- G11* (p.Gly11Ter), gnomAD 9-127612434-G-T, CADD 36.00
- G11G (p.Gly11Gly), rs1588211811, gnomAD 9-127612436-A-G, CADD 18.40
- G11D (p.Gly11Asp), gnomAD 9-127613268-CG-C, CADD 13.80
- G11V (p.Gly11Val), gnomAD 9-127613272-G-T, CADD 15.10
- E12D (p.Glu12Asp), rs796053378, ClinGen CA318901, ClinVar RCV000189628, ClinVar RCV006462031, REVEL 0.18, CADD 22.40, Conflicting interpretations, Early-infantile DEE; not provided
- E12K (p.Glu12Lys), gnomAD 9-127612437-G-A, REVEL 0.29, CADD 23.10
- E12G (p.Glu12Gly), gnomAD 9-127612438-A-G, REVEL 0.40, CADD 24.10
- K13N (p.Lys13Asn), cosmic curated COSV10592
- K13E (p.Lys13Glu), gnomAD 9-127612440-A-G, REVEL 0.36, CADD 22.80
- I14V (p.Ile14Val), TOPMed rs1427960857, gnomAD rs1427960857, REVEL 0.64, CADD 23.20
- M15I (p.Met15Ile), rs2539771319, ClinGen CA375176052, ClinVar RCV006472003, Uncertain significance, Early-infantile DEE
- M15K (p.Met15Lys), TOPMed rs1004281468, Uncertain significance, not provided; Early-infantile DEE
- M15V (p.Met15Val), ExAC rs765782410, TOPMed rs765782410, gnomAD rs765782410
- H16Q (p.His16Gln), NCI-TCGA Cosmic COSV1009, cosmic curated COSV10096, Variant assessed as somatic; moderate impact.
- H16R (p.His16Arg), ExAC rs571127140, TOPMed rs571127140, gnomAD rs571127140, REVEL 0.26, CADD 23.30
- H16Y (p.His16Tyr), rs2539771331, ClinGen CA375176057, ClinVar RCV006564036, Uncertain significance, Early-infantile DEE
- D17E (p.Asp17Glu), rs2539771360, ClinGen CA375176069, ClinVar RCV006560648, Uncertain significance, Early-infantile DEE
- D17H (p.Asp17His), cosmic curated COSV64815
- D17Y (p.Asp17Tyr), NCI-TCGA Cosmic COSV6481, Variant assessed as somatic; moderate impact.
- D17G (p.Asp17Gly), gnomAD 9-127651615-A-G, REVEL 0.38, CADD 22.30
- D17V (p.Asp17Val), gnomAD 9-127651615-A-T, REVEL 0.74, CADD 26.10
- V18M (p.Val18Met), rs2132436612, ClinGen CA375176070, ClinVar RCV006468987, Ensembl rs2132436612, AlphaMissense 0.84, MetaLR 0.61, Likely benign, Early-infantile DEE
- V18V (p.Val18Val), rs1296643979, gnomAD 9-127651619-G-A, CADD 10.30
- I19T (p.Ile19Thr), rs2539771391, ClinGen CA375176080, ClinVar RCV003142294, CADD 13.80, Uncertain significance, Developmental and epileptic encephalopathy, 4
- I19F (p.Ile19Phe), gnomAD 9-127613277-A-T, CADD 6.04
- I19L (p.Ile19Leu), rs1022262763, gnomAD 9-127613277-A-C, CADD 6.18
- I19V (p.Ile19Val), rs1022262763, gnomAD 9-127613277-A-G, CADD 6.50
- I19I (p.Ile19Ile), gnomAD 9-127613279-C-A, CADD 14.30
- K20M (p.Lys20Met), gnomAD 9-127651624-A-T, REVEL 0.37, CADD 24.70
- K20T (p.Lys20Thr), gnomAD 9-127651624-A-C, REVEL 0.21, CADD 22.30
- K21Q (p.Lys21Gln), TOPMed rs968835866, REVEL 0.27, CADD 23.10, Uncertain significance, not provided
- V22I (p.Val22Ile), gnomAD 9-127651629-G-A, REVEL 0.32, CADD 22.60
- K23N (p.Lys23Asn), gnomAD 9-127651634-G-C, REVEL 0.38, CADD 26.40
- K24E (p.Lys24Glu), rs2132436701, ClinGen CA375176113, ClinVar RCV001727487, Ensembl rs2132436701, AlphaMissense 0.32, MetaLR 0.46, Likely benign, not provided
- K25N (p.Lys25Asn), rs1410513659, ClinGen CA375176126, NCI-TCGA Cosmic COSV1009, cosmic curated COSV10096, REVEL 0.21, CADD 23.00, Uncertain significance, Early-infantile DEE
- K25Q (p.Lys25Gln), rs756787732, ClinGen CA5248209, ClinVar RCV006463750, ExAC rs756787732, REVEL 0.39, CADD 24.40, Uncertain significance, Early-infantile DEE
- K25K (p.Lys25Lys), rs1410513659, gnomAD 9-127651640-G-A, CADD 11.00
- G26R (p.Gly26Arg), NCI-TCGA TCGA novel, TOPMed rs1840556374, Variant assessed as somatic; moderate impact.
- E27* (p.Glu27Ter), rs1564346538, ClinGen CA375176134, ClinVar RCV000680112, ClinVar RCV006556532, Pathogenic
- E27E (p.Glu27Glu), gnomAD 9-127651646-A-G, CADD 9.24
- W28* (p.Trp28Ter), rs1064793984, ClinGen CA16618736, ClinVar RCV000481498, Ensembl rs1064793984, Pathogenic
- W28G (p.Trp28Gly), rs2539771553, ClinGen CA375176143, ClinVar RCV002280066, Pathogenic, not provided
- K29N (p.Lys29Asn), cosmic curated COSV64812
- V30M (p.Val30Met), rs1840653229, ClinGen CA375176169, ClinVar RCV006466346, Ensembl rs1840653229, AlphaMissense 0.95, MetaLR 0.78, Likely pathogenic, Early-infantile DEE
- L31P (p.Leu31Pro), rs2539777941, ClinVar RCV004595101, Likely pathogenic, Developmental and epileptic encephalopathy, 4
- L31L (p.Leu31Leu), gnomAD 9-127613286-C-T, CADD 8.09
- V32M (p.Val32Met), Ensembl rs1036081930, REVEL 0.80, CADD 27.50
- V32V (p.Val32Val), gnomAD 9-127653723-G-A, CADD 12.20
- V33E (p.Val33Glu), rs1840653547, ClinGen CA375176186, ClinVar RCV006464809, Ensembl rs1840653547, AlphaMissense 0.99, MetaLR 0.66, Likely pathogenic, Early-infantile DEE
- V33V (p.Val33Val), rs761031235, gnomAD 9-127653726-G-A, CADD 7.30
- D34N (p.Asp34Asn), rs2539777985, ClinGen CA375176189, ClinVar RCV004763720, ClinVar RCV006562397, Uncertain significance, not provided; Early-infantile DEE
- D34Y (p.Asp34Tyr), gnomAD 9-127653727-G-T, REVEL 0.95, CADD 32.00
- Q35* (p.Gln35Ter), cosmic curated COSV64812
- Q35H (p.Gln35His), TOPMed rs1840653903, gnomAD rs1840653903, REVEL 0.35, CADD 17.50
- L36* (p.Leu36Ter), rs1085307900, ClinGen CA375176209, cosmic curated COSV10821, ClinVar RCV000489814, Pathogenic
- L36L (p.Leu36Leu), rs759912722, gnomAD 9-127653733-T-C, CADD 10.80
- S37C (p.Ser37Cys), cosmic curated COSV64812
- M38I (p.Met38Ile), cosmic curated COSV10096
- M38T (p.Met38Thr), rs538684549, ClinGen CA201185127, ClinVar RCV006465993, 1000Genomes rs538684549, AlphaMissense 0.80, MetaLR 0.28, Uncertain significance, Early-infantile DEE
- R39K (p.Arg39Lys), Ensembl rs2132444480
- R39S (p.Arg39Ser), rs2132444493, ClinGen CA375176234, ClinVar RCV005742321, ClinVar RCV006558016, AlphaMissense 0.99, MetaLR 0.66, Uncertain significance, Early-infantile DEE; Inborn genetic diseases
- R39R (p.Arg39Arg), gnomAD 9-127613267-G-A, CADD 19.30
- R39G (p.Arg39Gly), gnomAD 9-127613267-GC-G, CADD 14.60
- R39W (p.Arg39Trp), rs1262053249, gnomAD 9-127613268-C-T, CADD 16.20
- R39P (p.Arg39Pro), rs989385275, gnomAD 9-127613269-G-C, CADD 15.10
- R39Q (p.Arg39Gln), gnomAD 9-127613269-G-A, CADD 15.30
- R39L (p.Arg39Leu), rs989385275, gnomAD 9-127613269-G-T, CADD 15.00
- M40K (p.Met40Lys), rs1840654963, ClinGen CA375176238, ClinVar RCV006466361, Ensembl rs1840654963, AlphaMissense 0.99, MetaLR 0.65, Uncertain significance, Early-infantile DEE
- M40L (p.Met40Leu), gnomAD rs1840654791, REVEL 0.41, CADD 22.70
- L41Q (p.Leu41Gln), rs2132444527, ClinGen CA375176246, ClinVar RCV001004708, AlphaMissense 0.99, MetaLR 0.81, Likely pathogenic, Developmental and epileptic encephalopathy, 4
- L41R (p.Leu41Arg), rs2132444527, ClinGen CA375176248, ClinVar RCV001726699, Ensembl rs2132444527, AlphaMissense 0.99, MetaLR 0.81, Pathogenic, Developmental and epileptic encephalopathy, 4
- L41L (p.Leu41Leu), rs766840783, gnomAD 9-127653750-G-C, CADD 2.67
- S42F (p.Ser42Phe), UniProt VAR 078631, Pathogenic, in DEE4
- S42P (p.Ser42Pro), rs886041668, ClinGen CA10603014, ClinVar RCV000334893, ClinVar RCV001265295, AlphaMissense 1.00, MetaLR 0.80, Pathogenic/Likely pathogenic, not provided; Early-infantile DEE
- S42Y (p.Ser42Tyr), rs1840655911, ClinGen CA375176251, ClinVar RCV001265296, Ensembl rs1840655911, AlphaMissense 0.99, MetaLR 0.79, Likely pathogenic, Infantile epilepsy syndrome
- S43F (p.Ser43Phe), cosmic curated COSV64812
- S43A (p.Ser43Ala), gnomAD 9-127653754-T-G, REVEL 0.44, CADD 22.70
- S43S (p.Ser43Ser), rs765727571, gnomAD 9-127653756-C-G, CADD 12.70
- C44C (p.Cys44Cys), rs373660650, gnomAD 9-127653759-C-T, CADD 14.40
- C45F (p.Cys45Phe), rs1840656429, ClinGen CA375176272, ClinVar RCV004047024, ClinVar RCV006469676, REVEL 0.80, CADD 24.50, Conflicting interpretations, Early-infantile DEE; Inborn genetic diseases
- C45C (p.Cys45Cys), rs1342454624, gnomAD 9-127653762-C-T, CADD 12.80
- K46E (p.Lys46Glu), rs1840656743, ClinGen CA375176277, ClinVar RCV001266945, Ensembl rs1840656743, AlphaMissense 0.98, MetaLR 0.76, Likely pathogenic, Inborn genetic diseases
- K46R (p.Lys46Arg), cosmic curated COSV64813
- T48T (p.Thr48Thr), rs1462537561, gnomAD 9-127653771-A-C, CADD 3.92
- D49A (p.Asp49Ala), gnomAD rs1840657200, REVEL 0.92, CADD 28.40
- D49H (p.Asp49His), rs1244732832, ClinGen CA375176300, ClinVar RCV003259039, ClinVar RCV005626304, REVEL 0.92, CADD 29.60, Conflicting interpretations, Multiple congenital anomalies/dysmorphic syndrome; Inborn genetic diseases; Earl
- I50V (p.Ile50Val), ExAC rs763601887, gnomAD rs763601887, REVEL 0.55, CADD 23.40
- I50I (p.Ile50Ile), rs1840657878, gnomAD 9-127653777-C-T, CADD 14.30
- M51I (p.Met51Ile), NCI-TCGA TCGA novel, REVEL 0.38, CADD 23.40, Variant assessed as somatic; moderate impact.
- M51V (p.Met51Val), NCI-TCGA TCGA novel, TOPMed rs1840658033, gnomAD rs1840658033, REVEL 0.45, CADD 22.30, Benign, Early-infantile DEE
- T52T (p.Thr52Thr), rs767019310, gnomAD 9-127653783-C-T, CADD 3.81
- E53* (p.Glu53Ter), rs749965674, ClinGen CA375176328, ClinVar RCV001038009, ExAC rs749965674, AlphaMissense 0.41, MetaLR 0.58, Pathogenic
- E53Q (p.Glu53Gln), rs749965674, ClinGen CA5248228, ClinVar RCV006471517, ExAC rs749965674, REVEL 0.56, AlphaMissense 0.41, Uncertain significance, Early-infantile DEE
- G54S (p.Gly54Ser), Ensembl rs1840658651
- I55T (p.Ile55Thr), rs2132444862, ClinGen CA375176344, ClinVar RCV001586328, Ensembl rs2132444862, AlphaMissense 0.99, MetaLR 0.75, Likely pathogenic, not provided
- T56=, rs1241441075, NCI-TCGA Cosmic COSV6481, Likely benign
- T56M (p.Thr56Met), NCI-TCGA Cosmic COSV6481, cosmic curated COSV64813, REVEL 0.90, CADD 33.00, Variant assessed as somatic; moderate impact.
- T56R (p.Thr56Arg), rs1554776228, ClinGen CA318913, ClinVar RCV006468821, Ensembl rs1554776228, AlphaMissense 0.99, MetaLR 0.76, Pathogenic, Early-infantile DEE
- T56S (p.Thr56Ser), cosmic curated COSV64813
- T56T (p.Thr56Thr), gnomAD 9-127653795-G-T, CADD 14.70
- I57T (p.Ile57Thr), rs2132460702, ClinGen CA375176367, ClinVar RCV001808017, Ensembl rs2132460702, AlphaMissense 0.98, MetaLR 0.62, Uncertain significance, Developmental and epileptic encephalopathy, 4
- E59K (p.Glu59Lys), rs2132460743, ClinGen CA375176376, ClinVar RCV003227051, ClinVar RCV006468615, AlphaMissense 1.00, MetaLR 0.75, Pathogenic, Early-infantile DEE; not provided
- I61T (p.Ile61Thr), rs2539791994, ClinGen CA375176395, ClinVar RCV006561934, REVEL 0.88, CADD 27.10, Likely benign, Early-infantile DEE
- I61V (p.Ile61Val), TOPMed rs1039353058, REVEL 0.38, CADD 22.40
- N62S (p.Asn62Ser), TOPMed rs1311665443, gnomAD rs1311665443, REVEL 0.22, CADD 21.60
- N62N (p.Asn62Asn), rs2132280044, gnomAD 9-127613291-C-T, CADD 15.90
- N62K (p.Asn62Lys), gnomAD 9-127613291-C-A, CADD 15.60
- R64C (p.Arg64Cys), rs760033783, NCI-TCGA Cosmic COSV6481, cosmic curated COSV64812, ExAC rs760033783, REVEL 0.73, CADD 26.90, Benign, Early-infantile DEE
- R64H (p.Arg64His), cosmic curated COSV64814, gnomAD rs1473863285, REVEL 0.55, CADD 25.90, Likely benign, Early-infantile DEE
- R65* (p.Arg65Ter), cosmic curated COSV64814
- R65G (p.Arg65Gly), rs1564348737, ClinGen CA375176419, ClinVar RCV000713554, Ensembl rs1564348737, AlphaMissense 1.00, MetaLR 0.78, Uncertain significance, not provided
- P67L (p.Pro67Leu), rs1182540431, ClinGen CA375176439, ClinVar RCV006562766, gnomAD rs1182540431, REVEL 0.82, CADD 26.20, Likely benign, Early-infantile DEE
- L68F (p.Leu68Phe), cosmic curated COSV10592
- P69S (p.Pro69Ser), NCI-TCGA TCGA novel, Uncertain significance, Developmental and epileptic encephalopathy, 4
- S70C (p.Ser70Cys), cosmic curated COSV64814
- S70I (p.Ser70Ile), ExAC rs753470248, gnomAD rs753470248
- S70T (p.Ser70Thr), ExAC rs753470248, gnomAD rs753470248, REVEL 0.22, CADD 22.30
- E72K (p.Glu72Lys), rs754668616, ClinGen CA5248251, ClinVar RCV001566722, ClinVar RCV006465937, REVEL 0.71, CADD 25.20, Conflicting interpretations, not provided; Early-infantile DEE
- E72Q (p.Glu72Gln), NCI-TCGA Cosmic COSV1009, cosmic curated COSV10096, Variant assessed as somatic; moderate impact.
- A73D (p.Ala73Asp), rs1554776686, ClinGen CA375176476, ClinVar RCV000658186, Ensembl rs1554776686, AlphaMissense 1.00, MetaLR 0.80, Uncertain significance, not provided
- V74A (p.Val74Ala), NCI-TCGA Cosmic COSV1009, cosmic curated COSV10096, Variant assessed as somatic; moderate impact.
- Y75* (p.Tyr75Ter), rs2132461012, ClinGen CA375176489, ClinVar RCV006468284, Ensembl rs2132461012, Pathogenic
- Y75C (p.Tyr75Cys), rs796053352, ClinGen CA318845, ClinVar RCV001265425, ClinVar RCV006555645, AlphaMissense 0.93, MetaLR 0.83, Likely pathogenic, Early-infantile DEE
- Y75H (p.Tyr75His), rs2539792278, ClinGen CA375176484, ClinVar RCV006563455, Pathogenic, Early-infantile DEE
- L76V (p.Leu76Val), rs2539792329, NCI-TCGA Cosmic COSV6481, cosmic curated COSV64812, ClinGen CA375176492, REVEL 0.69, CADD 24.60, Uncertain significance, Developmental and epileptic encephalopathy, 4
- I77T (p.Ile77Thr), rs2539792386, ClinGen CA375176500, ClinVar RCV006563002, Uncertain significance, Early-infantile DEE
- T78S (p.Thr78Ser), ExAC rs752547899, TOPMed rs752547899, gnomAD rs752547899, REVEL 0.30, CADD 19.40
- P79A (p.Pro79Ala), rs1462181047, NCI-TCGA Cosmic COSV6481, cosmic curated COSV64812, gnomAD rs1462181047, REVEL 0.94, CADD 24.60, Variant assessed as somatic; moderate impact.
- P79L (p.Pro79Leu), rs1588302912, ClinGen CA375176513, ClinVar RCV000988248, Ensembl rs1588302912, AlphaMissense 0.99, MetaLR 0.88, Likely pathogenic, Developmental and epileptic encephalopathy, 4
- S80F (p.Ser80Phe), cosmic curated COSV10821
- S80P (p.Ser80Pro), rs1840867221, ClinGen CA375176515, ClinVar RCV001260827, ClinVar RCV006557278, AlphaMissense 0.92, MetaLR 0.48, Uncertain significance, Intellectual disability; Early-infantile DEE
- E81* (p.Glu81Ter), rs1461664423, ClinGen CA375176522, ClinVar RCV000988249, TOPMed rs1461664423, AlphaMissense 0.12, MetaLR 0.56, Pathogenic
Public STXBP1 analysis runs
- STXBP1 analysis run — STXBP1 (823 variants) — completed 2026-08-18