EYA1 (Protein phosphatase EYA1) variants and mutations
EYA1 (also known as Protein phosphatase EYA1) is a human protein-coding gene encoding a protein phosphatase protein. It functions as a transcriptional coactivator and phosphatase in developmental programs that form the ear, kidney, and craniofacial structures. Haploinsufficiency causes branchio-oto-renal spectrum disorders with hearing loss, branchial anomalies, and variable renal malformations. This analysis covers 1,097 EYA1 variants and mutations. Of these, 64% have computational variant effect predictions. Disease context includes BOR syndrome, branchio-oto-renal syndrome, and branchiootic syndrome 1. Example EYA1 variants include M1?, E2K, and E2V.
Variant analysis overview
- Gene: EYA1
- Protein: Protein phosphatase EYA1
- UniProt accession: Q99502
- Organism: Homo sapiens
- Variants analyzed: 1097
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 909 unspecified-consequence records; 4 frameshift variants; 1 stop retained variant; 78 synonymous variants; 93 missense variants; 4 stop-gained variants; 3 splice-region variants; 3 in-frame deletions; 1 in-frame insertions; 3 substitution
- Prediction scores: 702 variants have prediction scores (64% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: BOR syndrome, branchio-oto-renal syndrome, branchiootic syndrome 1, otofaciocervical syndrome 1, otofaciocervical syndrome, Branchio-otic syndrome, neurodegenerative disease, Rare genetic deafness, hereditary disease, branchiooculofacial syndrome, type 2 diabetes mellitus, hearing loss disorder.
Protein structure and variant hotspots
- Protein features: 3 binding 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 EYA1 variants
Examples include M1?, E2K, E2V, M3I, M3L, M3R, D5A, D5N. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, cosmic curated COSV10733
- E2K (p.Glu2Lys), NCI-TCGA Cosmic COSV5816, cosmic curated COSV58161, Ensembl rs1586519835, Variant assessed as somatic; moderate impact.
- E2V (p.Glu2Val), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- M3I (p.Met3Ile), rs1826704843, ClinGen CA371529758, ClinVar RCV001196411, Ensembl rs1826704843, REVEL 0.53, MetaLR 0.83, Uncertain significance, Branchiootic syndrome 1; Otofaciocervical syndrome 1; Branchiootorenal syndrome
- M3L (p.Met3Leu), Ensembl rs2129069930
- M3R (p.Met3Arg), rs2537446532, ClinGen CA371529763, ClinVar RCV003758624, Uncertain significance, Melnick-Fraser syndrome
- D5A (p.Asp5Ala), ExAC rs767080375
- D5N (p.Asp5Asn), cosmic curated COSV10515, REVEL 0.57, MetaLR 0.88
- D5Y (p.Asp5Tyr), rs980123558, []
- L6P (p.Leu6Pro), NCI-TCGA Cosmic COSV5817, cosmic curated COSV58175, Variant assessed as somatic; moderate impact.
- S8N (p.Ser8Asn), TOPMed rs1393157586, gnomAD rs1393157586, REVEL 0.50, MetaLR 0.79, Conflicting interpretations, Branchiootorenal syndrome 1; Melnick-Fraser syndrome; Branchiootic syndrome 1
- P9L (p.Pro9Leu), rs766713665, ClinGen CA4779942, NCI-TCGA Cosmic COSV5816, cosmic curated COSV58165, REVEL 0.54, MetaLR 0.90, Conflicting interpretations, Melnick-Fraser syndrome; Branchiootorenal syndrome 1; Branchiootic syndrome 1
- P9R (p.Pro9Arg), ExAC rs766713665, TOPMed rs766713665, gnomAD rs766713665, Likely benign
- H10N (p.His10Asn), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10037, NCI-TCGA Cosmic COSV5816, Variant assessed as somatic; moderate impact.
- H10R (p.His10Arg), TOPMed rs1052858465, gnomAD rs1052858465, REVEL 0.48, MetaLR 0.74
- H10Y (p.His10Tyr), cosmic curated COSV58161
- S11G (p.Ser11Gly), Ensembl rs1826700768, REVEL 0.35, MetaLR 0.56
- S11N (p.Ser11Asn), rs1164012590, gnomAD rs1164012590, REVEL 0.46, MetaLR 0.52, Variant assessed as somatic; moderate impact.
- R12C (p.Arg12Cys), rs530921368, ClinGen CA179474515, ClinVar RCV001914199, ClinVar RCV002469431, REVEL 0.25, MetaLR 0.28, Conflicting interpretations, Inborn genetic diseases; Branchiootic syndrome 1; Branchiootorenal syndrome 1
- R12H (p.Arg12His), rs74720958, ClinGen CA4779938, cosmic curated COSV10038, ClinVar RCV000825672, REVEL 0.18, MetaLR 0.29, Conflicting interpretations, Melnick-Fraser syndrome; not specified; Otofaciocervical syndrome 1
- R12P (p.Arg12Pro), 1000Genomes rs74720958, ESP rs74720958, ExAC rs74720958, TOPMed rs74720958, REVEL 0.21, MetaLR 0.29, Likely benign, Melnick-Fraser syndrome
- L13M (p.Leu13Met), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- L13Q (p.Leu13Gln), ExAC rs768783796, gnomAD rs768783796, REVEL 0.27, MetaLR 0.25, Likely benign, Melnick-Fraser syndrome
- L13V (p.Leu13Val), ExAC rs776514587, gnomAD rs776514587, REVEL 0.07, MetaLR 0.13, Uncertain significance, Branchiootic syndrome 1; Otofaciocervical syndrome 1; Branchiootorenal syndrome
- S14R (p.Ser14Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S14T (p.Ser14Thr), Ensembl rs1028056830
- G15A (p.Gly15Ala), cosmic curated COSV10885
- S16G (p.Ser16Gly), cosmic curated COSV58169
- S17G (p.Ser17Gly), rs747231434, ClinGen CA4779935, ClinVar RCV000999043, ClinVar RCV001858894, REVEL 0.04, MetaLR 0.09, Conflicting interpretations, Branchiootic syndrome 1; Otofaciocervical syndrome 1; Branchiootorenal syndrome
- S17N (p.Ser17Asn), ExAC rs780483424, gnomAD rs780483424, REVEL 0.06, MetaLR 0.15
- E18K (p.Glu18Lys), NCI-TCGA Cosmic COSV5816, cosmic curated COSV58163, REVEL 0.09, MetaLR 0.14, Variant assessed as somatic; moderate impact.
- S19C (p.Ser19Cys), rs2129069830, ClinGen CA371529501, ClinVar RCV001910373, Ensembl rs2129069830, REVEL 0.29, MetaLR 0.26, Uncertain significance, Melnick-Fraser syndrome
- P20A (p.Pro20Ala), rs1445404, ClinGen CA142606, cosmic curated COSV58160, ClinVar RCV000041394, REVEL 0.27, MetaLR 0.00, Benign, Melnick-Fraser syndrome; not specified; not provided
- P20L (p.Pro20Leu), cosmic curated COSV99063, REVEL 0.36, MetaLR 0.19
- P20S (p.Pro20Ser), 1000Genomes rs1445404, ESP rs1445404, ExAC rs1445404, TOPMed rs1445404, REVEL 0.25, MetaLR 0.14, Benign
- P20T (p.Pro20Thr), 1000Genomes rs1445404, ESP rs1445404, ExAC rs1445404, TOPMed rs1445404, REVEL 0.32, MetaLR 0.20, Benign
- S21R (p.Ser21Arg), gnomAD rs1826695189, REVEL 0.07, MetaLR 0.10
- G22A (p.Gly22Ala), cosmic curated COSV10038
- G22D (p.Gly22Asp), rs727503049, ClinGen CA176088, ClinVar RCV000150678, ClinVar RCV002505146, REVEL 0.25, MetaLR 0.15, Conflicting interpretations, not specified; Inborn genetic diseases; Melnick-Fraser syndrome
- P23H (p.Pro23His), cosmic curated COSV99063
- L25I (p.Leu25Ile), ExAC rs752696368, gnomAD rs752696368, REVEL 0.07, MetaLR 0.23
- G26C (p.Gly26Cys), rs199664417, NCI-TCGA Cosmic COSV1003, cosmic curated COSV10038, NCI-TCGA Cosmic COSV5817, REVEL 0.39, MetaLR 0.54, Likely benign
- G26D (p.Gly26Asp), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10037, Ensembl rs2129069787, Variant assessed as somatic; moderate impact.
- G26R (p.Gly26Arg), NCI-TCGA Cosmic COSV1003, NCI-TCGA Cosmic COSV5817, Variant assessed as somatic; moderate impact.
- G26S (p.Gly26Ser), rs199664417, ClinGen CA4779929, NCI-TCGA Cosmic COSV1003, NCI-TCGA Cosmic COSV5817, REVEL 0.44, MetaLR 0.34, Conflicting interpretations, Branchiootic syndrome 1; Otofaciocervical syndrome 1; Branchiootorenal syndrome
- N27T (p.Asn27Thr), ExAC rs751187504, gnomAD rs751187504, REVEL 0.28, MetaLR 0.36
- S28C (p.Ser28Cys), ExAC rs558089479, TOPMed rs558089479, gnomAD rs558089479, REVEL 0.41, MetaLR 0.69
- S28T (p.Ser28Thr), cosmic curated COSV58159
- I30M (p.Ile30Met), TOPMed rs1486534014, gnomAD rs1486534014
- I30V (p.Ile30Val), rs1554565600, ClinGen CA371529332, cosmic curated COSV10037, ClinVar RCV000607103, AlphaMissense 0.10, MetaLR 0.12, Uncertain significance, not specified; not provided
- N31K (p.Asn31Lys), Ensembl rs2129069768, REVEL 0.04, MetaLR 0.11
- N31S (p.Asn31Ser), Ensembl rs1826690625, REVEL 0.12, MetaLR 0.09
- S32I (p.Ser32Ile), cosmic curated COSV58158
- N33K (p.Asn33Lys), TOPMed rs1826690311
- T36I (p.Thr36Ile), rs727503048, ClinGen CA176085, ClinVar RCV000150677, ClinVar RCV001577879, REVEL 0.35, MetaLR 0.23, Conflicting interpretations, not specified; Otofaciocervical syndrome 1; Branchiootic syndrome 1
- N38D (p.Asn38Asp), rs765646278, ClinGen CA4779925, ClinVar RCV001547552, ClinVar RCV002032571, REVEL 0.13, MetaLR 0.37, Likely benign, not provided; Melnick-Fraser syndrome
- N38I (p.Asn38Ile), ExAC rs750274491, TOPMed rs750274491, gnomAD rs750274491, REVEL 0.30, MetaLR 0.38, Uncertain significance
- N38S (p.Asn38Ser), rs750274491, ClinGen CA4779924, NCI-TCGA Cosmic COSV5816, cosmic curated COSV58160, REVEL 0.14, MetaLR 0.32, Uncertain significance, Melnick-Fraser syndrome; Inborn genetic diseases
- G39D (p.Gly39Asp), rs267601985, NCI-TCGA Cosmic COSV5816, cosmic curated COSV58168, ClinVar RCV006588965, AlphaMissense 0.33, MetaLR 0.41, Uncertain significance, Melnick-Fraser syndrome
- G39S (p.Gly39Ser), cosmic curated COSV10733, REVEL 0.27, MetaLR 0.35
- T40A (p.Thr40Ala), TOPMed rs1196497532, gnomAD rs1196497532, REVEL 0.42, MetaLR 0.73
- T40P (p.Thr40Pro), TOPMed rs1196497532, gnomAD rs1196497532
- E41K (p.Glu41Lys), rs561111097, ClinGen CA4779923, NCI-TCGA Cosmic COSV5817, cosmic curated COSV58171, REVEL 0.48, MetaLR 0.58, Likely benign, Melnick-Fraser syndrome; not specified
- E41Q (p.Glu41Gln), rs561111097, ClinGen CA4779922, ClinVar RCV000234887, ClinVar RCV002518414, REVEL 0.37, MetaLR 0.61, Conflicting interpretations, Melnick-Fraser syndrome; Renal hypoplasia
- V42I (p.Val42Ile), cosmic curated COSV10733, REVEL 0.12, MetaLR 0.22
- K43T (p.Lys43Thr), rs1824212559, ClinGen CA371469360, ClinVar RCV003837882, Ensembl rs1824212559, AlphaMissense 0.57, MetaLR 0.40, Uncertain significance, Melnick-Fraser syndrome
- T44I (p.Thr44Ile), rs774402195, ExAC rs774402195, TOPMed rs774402195, gnomAD rs774402195, REVEL 0.38, MetaLR 0.41, Variant assessed as somatic; moderate impact.
- E45K (p.Glu45Lys), gnomAD rs1373021054, REVEL 0.32, MetaLR 0.40
- M47I (p.Met47Ile), rs1563486266, ClinGen CA371469328, ClinVar RCV003304387, Ensembl rs1563486266, REVEL 0.24, MetaLR 0.31, Uncertain significance, Inborn genetic diseases
- M47L (p.Met47Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- M47T (p.Met47Thr), TOPMed rs1323652552, gnomAD rs1323652552, REVEL 0.34, MetaLR 0.27
- S48R (p.Ser48Arg), cosmic curated COSV58177
- S49I (p.Ser49Ile), cosmic curated COSV10460, REVEL 0.32, MetaLR 0.31
- S49N (p.Ser49Asn), TOPMed rs958156575, REVEL 0.07, MetaLR 0.18
- S49R (p.Ser49Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S50C (p.Ser50Cys), NCI-TCGA Cosmic COSV5816, cosmic curated COSV58164, Variant assessed as somatic; moderate impact.
- E51K (p.Glu51Lys), NCI-TCGA TCGA novel, REVEL 0.09, MetaLR 0.23, Variant assessed as somatic; moderate impact.
- T52I (p.Thr52Ile), 1000Genomes rs200206302, ExAC rs200206302, gnomAD rs200206302, REVEL 0.14, MetaLR 0.16
- T52K (p.Thr52Lys), NCI-TCGA Cosmic COSV5817, cosmic curated COSV58170, Variant assessed as somatic; moderate impact.
- A53D (p.Ala53Asp), ExAC rs776352141, TOPMed rs776352141, gnomAD rs776352141, Uncertain significance
- A53T (p.Ala53Thr), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10038, REVEL 0.06, MetaLR 0.10, Variant assessed as somatic; moderate impact.
- A53V (p.Ala53Val), rs776352141, ClinGen CA4779874, ClinVar RCV002583111, ClinVar RCV004725311, REVEL 0.10, MetaLR 0.13, Uncertain significance, Melnick-Fraser syndrome; not provided
- T55A (p.Thr55Ala), rs139194909, ClinGen CA4779872, ClinVar RCV001756301, ClinVar RCV003771907, REVEL 0.07, MetaLR 0.17, Conflicting interpretations, Branchiootorenal syndrome 1; Branchiootic syndrome 1; Otofaciocervical syndrome
- T55M (p.Thr55Met), rs201434219, ClinGen CA182790, ClinVar RCV000155446, ClinVar RCV000392984, REVEL 0.34, MetaLR 0.30, Conflicting interpretations, not specified; not provided; Branchiootic syndrome 1
- T56A (p.Thr56Ala), gnomAD rs1248918883, REVEL 0.05, MetaLR 0.13
- T56I (p.Thr56Ile), gnomAD rs1199697219
- D58E (p.Asp58Glu), rs370509332, ESP rs370509332, ExAC rs370509332, TOPMed rs370509332, REVEL 0.16, MetaLR 0.32, Likely benign
- D58N (p.Asp58Asn), rs756885537, NCI-TCGA Cosmic COSV5816, cosmic curated COSV58166, ExAC rs756885537, REVEL 0.14, MetaLR 0.40, Uncertain significance, Branchiootic syndrome 1; Otofaciocervical syndrome 1; Branchiootorenal syndrome
- G59E (p.Gly59Glu), NCI-TCGA Cosmic COSV5817, cosmic curated COSV58176, Ensembl rs2129047018, Variant assessed as somatic; moderate impact.
- G59R (p.Gly59Arg), rs146216506, ClinGen CA4779866, cosmic curated COSV58168, ClinVar RCV001558781, REVEL 0.32, MetaLR 0.27, Uncertain significance, Melnick-Fraser syndrome; not provided
- G59W (p.Gly59Trp), cosmic curated COSV58165
- S60P (p.Ser60Pro), Ensembl rs1824204061, REVEL 0.08, MetaLR 0.14
- S60Y (p.Ser60Tyr), cosmic curated COSV10037, 1000Genomes rs2129047013, REVEL 0.19, MetaLR 0.20
- N62D (p.Asn62Asp), Ensembl rs2129047006
- N63H (p.Asn63His), Ensembl rs2129046999
- F64L (p.Phe64Leu), NCI-TCGA Cosmic COSV5815, cosmic curated COSV58159, Variant assessed as somatic; moderate impact.
- S65* (p.Ser65Ter), cosmic curated COSV58159, NCI-TCGA Cosmic COSV1003, cosmic curated COSV10038, NCI-TCGA Cosmic COSV5815, Variant assessed as somatic; high impact.
- S65L (p.Ser65Leu), TOPMed rs1389200174, gnomAD rs1389200174, REVEL 0.36, MetaLR 0.24
- G66C (p.Gly66Cys), rs886063089, ClinGen CA10631496, ClinVar RCV000303649, ClinVar RCV000342060, REVEL 0.41, MetaLR 0.43, Uncertain significance, Branchiootic syndrome 1; Otofaciocervical syndrome 1
- G66D (p.Gly66Asp), cosmic curated COSV58171, REVEL 0.36, MetaLR 0.35
- G66V (p.Gly66Val), rs149289196, ClinGen CA4779865, cosmic curated COSV10610, ClinVar RCV002469740, REVEL 0.43, MetaLR 0.40, Uncertain significance, not provided
- A68E (p.Ala68Glu), cosmic curated COSV58159, REVEL 0.19, MetaLR 0.13
- A68G (p.Ala68Gly), rs1822657436, ClinGen CA371469089, ClinVar RCV001196644, Ensembl rs1822657436, AlphaMissense 0.12, MetaLR 0.12, Uncertain significance, Otofaciocervical syndrome 1
- A68P (p.Ala68Pro), TOPMed rs1169615269, gnomAD rs1169615269
- A68S (p.Ala68Ser), TOPMed rs1169615269, gnomAD rs1169615269, REVEL 0.08, MetaLR 0.16
- I69L (p.Ile69Leu), TOPMed rs1032162749, gnomAD rs1032162749, REVEL 0.08, MetaLR 0.25
- I69T (p.Ile69Thr), rs371059560, ClinGen CA4779849, ClinVar RCV003760436, ClinVar RCV004980992, REVEL 0.29, MetaLR 0.45, Uncertain significance, Melnick-Fraser syndrome; Inborn genetic diseases
- I69V (p.Ile69Val), TOPMed rs1032162749, gnomAD rs1032162749, REVEL 0.09, MetaLR 0.29
- G70E (p.Gly70Glu), cosmic curated COSV10441, gnomAD rs1822654842, REVEL 0.26, MetaLR 0.22
- G70R (p.Gly70Arg), NCI-TCGA Cosmic COSV5816, cosmic curated COSV58166, Variant assessed as somatic; moderate impact.
- S71N (p.Ser71Asn), rs1462564075, TOPMed rs1462564075, REVEL 0.11, MetaLR 0.31, Variant assessed as somatic; moderate impact.
- S72G (p.Ser72Gly), rs1275882788, NCI-TCGA Cosmic COSV5816, cosmic curated COSV58164, TOPMed rs1275882788, REVEL 0.34, MetaLR 0.47, Variant assessed as somatic; moderate impact.
- S73N (p.Ser73Asn), rs1429110987, ClinGen CA371469024, ClinVar RCV002972008, TOPMed rs1429110987, REVEL 0.14, MetaLR 0.11, Uncertain significance, Melnick-Fraser syndrome
- S73R (p.Ser73Arg), TOPMed rs1201735320
- F74C (p.Phe74Cys), cosmic curated COSV10640
- S75C (p.Ser75Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- P76L (p.Pro76Leu), NCI-TCGA Cosmic COSV5816, cosmic curated COSV58163, REVEL 0.39, MetaLR 0.45, Variant assessed as somatic; moderate impact.
- P76S (p.Pro76Ser), gnomAD rs1822652918, REVEL 0.27, MetaLR 0.40
- R77* (p.Arg77Ter), rs200164773, ClinGen CA371468970, NCI-TCGA Cosmic COSV5816, cosmic curated COSV58164, CADD 35.00, Pathogenic
- R77Q (p.Arg77Gln), rs770356158, ClinGen CA4779848, NCI-TCGA Cosmic COSV5816, cosmic curated COSV58169, REVEL 0.29, MetaLR 0.47, Conflicting interpretations, Melnick-Fraser syndrome; Otofaciocervical syndrome 1; Branchiootic syndrome 1
- P78L (p.Pro78Leu), cosmic curated COSV10460, REVEL 0.06, MetaLR 0.14
- P78R (p.Pro78Arg), gnomAD rs1414412230, REVEL 0.07, MetaLR 0.15
- P78S (p.Pro78Ser), cosmic curated COSV10515
- T79A (p.Thr79Ala), rs1554550645, ClinGen CA371468949, ClinVar RCV000522348, ClinVar RCV002481735, REVEL 0.10, MetaLR 0.02, Uncertain significance, not provided; Melnick-Fraser syndrome; Branchiootic syndrome 1
- Q81* (p.Gln81Ter), rs1554550637, ClinGen CA371468924, ClinVar RCV000600507, Ensembl rs1554550637, Pathogenic
- Q81R (p.Gln81Arg), TOPMed rs1822649069, REVEL 0.18, MetaLR 0.47
- F82S (p.Phe82Ser), ExAC rs777629266, gnomAD rs777629266
- F82V (p.Phe82Val), cosmic curated COSV58171
- F82Y (p.Phe82Tyr), ExAC rs777629266, gnomAD rs777629266, REVEL 0.24, MetaLR 0.04
- S83C (p.Ser83Cys), rs748482012, ClinGen CA4779844, ClinVar RCV001887425, ExAC rs748482012, REVEL 0.39, MetaLR 0.51, Uncertain significance, Melnick-Fraser syndrome
- S83F (p.Ser83Phe), ExAC rs748482012, TOPMed rs748482012, gnomAD rs748482012, REVEL 0.41, MetaLR 0.51, Uncertain significance
- S83P (p.Ser83Pro), gnomAD rs1191745624
- S83T (p.Ser83Thr), cosmic curated COSV58171
- P85S (p.Pro85Ser), TOPMed rs1237828849, gnomAD rs1237828849, REVEL 0.13, MetaLR 0.15
- Q86R (p.Gln86Arg), ExAC rs781429176, TOPMed rs781429176, gnomAD rs781429176, REVEL 0.26, MetaLR 0.35
- I87F (p.Ile87Phe), cosmic curated COSV10038, Ensembl rs1822645441, REVEL 0.45, MetaLR 0.56
- I87T (p.Ile87Thr), ExAC rs755452077, gnomAD rs755452077, REVEL 0.51, MetaLR 0.52
- I87V (p.Ile87Val), NCI-TCGA Cosmic COSV1003, Variant assessed as somatic; moderate impact.
- Y88* (p.Tyr88Ter), cosmic curated COSV58165
- Y88H (p.Tyr88His), 1000Genomes rs534707284, ExAC rs534707284, gnomAD rs534707284, REVEL 0.55, MetaLR 0.71
- P89L (p.Pro89Leu), rs368351103, ClinGen CA4779839, ClinVar RCV000825756, ClinVar RCV001869269, REVEL 0.47, MetaLR 0.74, Conflicting interpretations, Melnick-Fraser syndrome; Branchiootic syndrome 1; Branchiootorenal syndrome 1
- P89S (p.Pro89Ser), gnomAD rs1255833754, REVEL 0.32, MetaLR 0.65
- S90F (p.Ser90Phe), gnomAD rs1379371014, REVEL 0.58, MetaLR 0.73
- N91D (p.Asn91Asp), rs750621028, ClinGen CA4779838, cosmic curated COSV10037, ClinVar RCV004385695, REVEL 0.39, MetaLR 0.72, Uncertain significance, Inborn genetic diseases
- N91K (p.Asn91Lys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- N91S (p.Asn91Ser), rs960785529, Uncertain significance
- P93S (p.Pro93Ser), cosmic curated COSV58156, REVEL 0.22, MetaLR 0.43
- Y94H (p.Tyr94His), cosmic curated COSV10962
- P95L (p.Pro95Leu), ExAC rs759310166, TOPMed rs759310166, gnomAD rs759310166, REVEL 0.74, MetaLR 0.74, Conflicting interpretations, Inborn genetic diseases; Melnick-Fraser syndrome; Branchiootic syndrome 1
- P95Q (p.Pro95Gln), ExAC rs759310166, TOPMed rs759310166, gnomAD rs759310166, REVEL 0.65, MetaLR 0.78, Uncertain significance, in BOR1
- P95S (p.Pro95Ser), cosmic curated COSV10515, UniProt VAR 064942, Pathogenic, in BOR1
- H96L (p.His96Leu), ESP rs377434964, ExAC rs377434964, gnomAD rs377434964, Uncertain significance
- H96R (p.His96Arg), rs377434964, ClinGen CA4779815, ClinVar RCV001764958, ESP rs377434964, REVEL 0.64, MetaLR 0.71, Uncertain significance, not provided
- I97T (p.Ile97Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- I97V (p.Ile97Val), rs1422583050, ClinGen CA371468688, ClinVar RCV001932776, ClinVar RCV002478314, REVEL 0.44, MetaLR 0.71, Uncertain significance, Melnick-Fraser syndrome; Branchiootorenal syndrome 1; Branchiootic syndrome 1
- L98F (p.Leu98Phe), ExAC rs766184209, TOPMed rs766184209, gnomAD rs766184209, REVEL 0.59, MetaLR 0.78
- P99L (p.Pro99Leu), rs763005068, ClinGen CA371468673, ClinVar RCV003325079, ClinVar RCV003759820, REVEL 0.59, MetaLR 0.67, Conflicting interpretations, not provided; Melnick-Fraser syndrome
- P99R (p.Pro99Arg), ExAC rs763005068, TOPMed rs763005068, gnomAD rs763005068, REVEL 0.63, MetaLR 0.68, Likely benign
- P99S (p.Pro99Ser), NCI-TCGA Cosmic COSV5817, cosmic curated COSV58170, Variant assessed as somatic; moderate impact.
- T100I (p.Thr100Ile), rs373501480, ClinGen CA371468668, ClinVar RCV002467291, ESP rs373501480, REVEL 0.45, MetaLR 0.68, Uncertain significance, not provided
- T100N (p.Thr100Asn), rs373501480, ClinGen CA184017, ClinVar RCV000156019, ClinVar RCV000281370, REVEL 0.28, MetaLR 0.55, Conflicting interpretations, Branchiootic syndrome 1; Otofaciocervical syndrome 1; EYA1-related disorder
- P101A (p.Pro101Ala), ESP rs138603867, ExAC rs138603867, TOPMed rs138603867, gnomAD rs138603867, REVEL 0.56, MetaLR 0.77
- P101L (p.Pro101Leu), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10037, REVEL 0.67, MetaLR 0.78, Uncertain significance, Branchiootic syndrome 1; Otofaciocervical syndrome 1; Branchiootorenal syndrome
- P101S (p.Pro101Ser), ESP rs138603867, ExAC rs138603867, TOPMed rs138603867, gnomAD rs138603867, REVEL 0.54, MetaLR 0.77
- S102F (p.Ser102Phe), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10037, Variant assessed as somatic; moderate impact.
- S102Y (p.Ser102Tyr), NCI-TCGA Cosmic COSV1003, Variant assessed as somatic; moderate impact.
- S103A (p.Ser103Ala), gnomAD rs1488509440
- S103L (p.Ser103Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T105S (p.Thr105Ser), NCI-TCGA Cosmic COSV5817, cosmic curated COSV58174, Variant assessed as somatic; moderate impact.
- M106T (p.Met106Thr), rs2129031597, ClinGen CA371468616, ClinVar RCV002214475, Ensembl rs2129031597, AlphaMissense 0.53, MetaLR 0.59, Uncertain significance, not provided
- M106V (p.Met106Val), Ensembl rs1822592144, REVEL 0.51, MetaLR 0.62
- A107G (p.Ala107Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- A107T (p.Ala107Thr), cosmic curated COSV58176, TOPMed rs1413761721, gnomAD rs1413761721, REVEL 0.36, MetaLR 0.49
- A108T (p.Ala108Thr), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10038, Variant assessed as somatic; moderate impact.
- Y109C (p.Tyr109Cys), gnomAD rs1489979978, REVEL 0.76, MetaLR 0.77
- Y109H (p.Tyr109His), rs141779040, ClinGen CA4779810, ClinVar RCV000294529, ClinVar RCV000335524, REVEL 0.68, MetaLR 0.77, Conflicting interpretations, not specified; EYA1-related disorder; not provided
- G110E (p.Gly110Glu), ExAC rs769041202, gnomAD rs769041202, REVEL 0.69, MetaLR 0.79
- G110V (p.Gly110Val), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10037, Variant assessed as somatic; moderate impact.
- Q113K (p.Gln113Lys), ExAC rs747371845, gnomAD rs747371845, REVEL 0.64, MetaLR 0.84
- Q113R (p.Gln113Arg), 1000Genomes rs184596522
Public EYA1 analysis runs
- EYA1 analysis run — EYA1 (1,097 variants) — completed 2026-08-22