USH1C (Harmonin) variants and mutations
USH1C (also known as Harmonin) is a human protein-coding gene encoding a harmonin protein. It organizes protein complexes in inner-ear hair-cell stereocilia and photoreceptor structures. Biallelic pathogenic variants cause Usher syndrome type 1C with congenital severe hearing loss and progressive retinitis pigmentosa, or in some alleles isolated deafness. This analysis covers 937 USH1C variants and mutations. Of these, 61% have computational variant effect predictions. Disease context includes Usher syndrome type 1C, autosomal recessive nonsyndromic hearing loss 18A, and Usher syndrome. Example USH1C variants include M1V, D2E, and R3*.
Variant analysis overview
- Gene: USH1C
- Protein: Harmonin
- UniProt accession: Q9Y6N9
- Organism: Homo sapiens
- Variants analyzed: 937
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 935 unspecified-consequence records; 3 stop lost; 2 substitution
- Prediction scores: 574 variants have prediction scores (61% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Usher syndrome type 1C, autosomal recessive nonsyndromic hearing loss 18A, Usher syndrome, Usher syndrome type 1, deafness, Retinal dystrophy, hearing loss, autosomal recessive, Usher syndrome type 2, Rare genetic deafness, retinitis pigmentosa, hereditary disease, hearing loss disorder.
Protein structure and variant hotspots
- Protein features: 3 domains; 1 post-translational modification sites.
- Structural context: 422 variants have structural context.
- Experimental data: 84 protein positions have experimental scores. Source: USH1C PDZ domain domainome 1.0.
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 USH1C variants
Examples include M1V, D2E, R3*, R3G, R3Q, R3X, K4N, K4T. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1V (p.Met1Val), rs1554965967, ClinGen CA379805399, ClinVar RCV000669702, MetaLR 0.19, MetaSVM -0.75, Likely pathogenic, Autosomal recessive nonsyndromic hearing loss 18A; Usher syndrome type 1C
- D2E (p.Asp2Glu), ExAC rs753871690, gnomAD rs753871690, REVEL 0.14, CADD 18.90, Likely benign
- R3* (p.Arg3Ter), rs876657624, ClinGen CA10575817, ClinVar RCV000240666, TOPMed rs876657624, CADD 38.00, Pathogenic
- R3G (p.Arg3Gly), cosmic curated COSV50024, TOPMed rs876657624, gnomAD rs876657624, Pathogenic
- R3Q (p.Arg3Gln), NCI-TCGA Cosmic COSV5001, cosmic curated COSV50014, Variant assessed as somatic; moderate impact.
- R3X, rs876657624, Conflicting interpretations
- K4N (p.Lys4Asn), gnomAD rs1307084632
- K4T (p.Lys4Thr), TOPMed rs1181091798, gnomAD rs1181091798, REVEL 0.15, CADD 23.30
- V5G (p.Val5Gly), rs1851606530, ClinGen CA379805207, ClinVar RCV002572990, TOPMed rs1851606530, REVEL 0.24, CADD 32.00, Uncertain significance, not provided
- A6T (p.Ala6Thr), cosmic curated COSV50014
- R7G (p.Arg7Gly), rs2497325239, ClinGen CA379805174, ClinVar RCV004484409, Uncertain significance, Inborn genetic diseases
- R7P (p.Arg7Pro), ExAC rs777396814, TOPMed rs777396814, gnomAD rs777396814, Uncertain significance
- R7Q (p.Arg7Gln), rs777396814, ClinGen CA5905294, ClinVar RCV002714927, ExAC rs777396814, REVEL 0.06, CADD 24.00, Uncertain significance, not provided
- E8* (p.Glu8Ter), cosmic curated COSV10437
- R10L (p.Arg10Leu), TOPMed rs1457882210, gnomAD rs1457882210, REVEL 0.16, CADD 25.30
- R10Q (p.Arg10Gln), TOPMed rs1457882210, gnomAD rs1457882210, REVEL 0.07, CADD 25.20
- R10W (p.Arg10Trp), NCI-TCGA TCGA novel, REVEL 0.20, CADD 33.00, Variant assessed as somatic; moderate impact.
- H11N (p.His11Asn), gnomAD rs1322658934, REVEL 0.08, CADD 23.90
- H11R (p.His11Arg), TOPMed rs1161954752, gnomAD rs1161954752, REVEL 0.16, CADD 24.90
- K12N (p.Lys12Asn), NCI-TCGA Cosmic COSV9913, cosmic curated COSV99139, Variant assessed as somatic; moderate impact.
- V13=, NCI-TCGA Cosmic COSV5003, NCI-TCGA Cosmic COSV9914, Variant assessed as somatic; low impact.
- V13A (p.Val13Ala), ExAC rs757473472, gnomAD rs757473472, REVEL 0.39, CADD 25.50, Likely pathogenic, Autosomal recessive nonsyndromic hearing loss 18A
- D14G (p.Asp14Gly), ExAC rs753946678, gnomAD rs753946678, REVEL 0.20, CADD 28.30, Uncertain significance, Inborn genetic diseases
- D14H (p.Asp14His), TOPMed rs1305058607, REVEL 0.09, CADD 27.00
- D14N (p.Asp14Asn), cosmic curated COSV10452, TOPMed rs1305058607, REVEL 0.06, CADD 22.40
- I17V (p.Ile17Val), rs1179635643, ClinGen CA379800944, ClinVar RCV001323281, gnomAD rs1179635643, REVEL 0.06, CADD 23.40, Uncertain significance, not provided
- E18K (p.Glu18Lys), cosmic curated COSV50019, REVEL 0.12, CADD 25.50
- D20Y (p.Asp20Tyr), TOPMed rs1380387191, REVEL 0.41, CADD 28.10
- A21G (p.Ala21Gly), ExAC rs747629737
- A21S (p.Ala21Ser), cosmic curated COSV10720, 1000Genomes rs181215175, ExAC rs181215175, REVEL 0.32, CADD 25.30
- E22* (p.Glu22Ter), cosmic curated COSV99140
- E22A (p.Glu22Ala), ExAC rs753180549, gnomAD rs753180549, REVEL 0.49, CADD 27.10
- E22G (p.Glu22Gly), ExAC rs753180549, gnomAD rs753180549, REVEL 0.49, CADD 32.00
- K23N (p.Lys23Asn), NCI-TCGA TCGA novel, REVEL 0.14, CADD 24.40, Variant assessed as somatic; moderate impact.
- D24E (p.Asp24Glu), ExAC rs759929001, gnomAD rs759929001, REVEL 0.24, CADD 22.80, Uncertain significance, Inborn genetic diseases
- D24N (p.Asp24Asn), cosmic curated COSV10452, TOPMed rs1851070793
- Y25* (p.Tyr25Ter), rs2497241374, ClinGen CA379800646, ClinVar RCV003702644, ClinVar RCV005609067, CADD 36.00, Pathogenic
- Y25C (p.Tyr25Cys), rs536191185, ClinGen CA5905189, ClinVar RCV001898706, 1000Genomes rs536191185, REVEL 0.50, CADD 28.70, Uncertain significance, not provided
- Y25H (p.Tyr25His), rs751983859, ClinGen CA5905190, ClinVar RCV001986415, ExAC rs751983859, REVEL 0.45, CADD 27.50, Uncertain significance, not provided
- L26F (p.Leu26Phe), rs267602805, ClinGen CA218466943, NCI-TCGA Cosmic COSV5001, cosmic curated COSV50014, REVEL 0.24, CADD 23.70, Uncertain significance, not provided
- Y27* (p.Tyr27Ter), rs2497241282, ClinGen CA379800535, ClinVar RCV002306741, Likely pathogenic
- Y27H (p.Tyr27His), gnomAD rs1222503025, REVEL 0.30, CADD 27.40
- D28N (p.Asp28Asn), ESP rs143192514, ExAC rs143192514, gnomAD rs143192514, REVEL 0.19, CADD 29.00, Uncertain significance, Inborn genetic diseases
- D28V (p.Asp28Val), Ensembl rs1851069813, REVEL 0.54, CADD 29.50
- D28Y (p.Asp28Tyr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V29A (p.Val29Ala), gnomAD rs1225585780, REVEL 0.39, CADD 24.80
- R31* (p.Arg31Ter), rs121908370, ClinGen CA253419, cosmic curated COSV50016, ClinVar RCV000005453, CADD 43.00, Pathogenic
- R31G (p.Arg31Gly), ExAC rs121908370, TOPMed rs121908370, gnomAD rs121908370, REVEL 0.58, CADD 32.00, Pathogenic
- R31Q (p.Arg31Gln), rs776511246, ClinGen CA5905185, NCI-TCGA Cosmic COSV5001, cosmic curated COSV50018, REVEL 0.30, CADD 29.00, Conflicting interpretations, not provided; Usher syndrome type 1
- M32I (p.Met32Ile), rs1294493185, ClinGen CA379800359, ClinVar RCV003155719, TOPMed rs1294493185, AlphaMissense 0.83, MetaLR 0.12, Uncertain significance, not specified
- M32K (p.Met32Lys), ESP rs376949470, ExAC rs376949470, TOPMed rs376949470, gnomAD rs376949470, Uncertain significance
- M32T (p.Met32Thr), rs376949470, ClinGen CA5905184, ClinVar RCV002588601, ESP rs376949470, AlphaMissense 0.79, MetaLR 0.13, Uncertain significance, not provided
- H34N (p.His34Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- H34R (p.His34Arg), rs75157409, ClinGen CA142283, ClinVar RCV000041246, ClinVar RCV000959167, REVEL 0.29, CADD 25.30, Benign/Likely benign, not specified; not provided; Usher syndrome type 1C
- Q35* (p.Gln35Ter), TOPMed rs1477925627, Uncertain significance
- Q35H (p.Gln35His), rs369151395, ClinGen CA218465486, ClinVar RCV000728072, ESP rs369151395, REVEL 0.07, CADD 22.90, Uncertain significance, not provided
- Q35K (p.Gln35Lys), rs1477925627, ClinGen CA379800286, cosmic curated COSV50028, ClinVar RCV002027706, AlphaMissense 0.18, MetaLR 0.06, Uncertain significance, not provided
- Q35R (p.Gln35Arg), NCI-TCGA Cosmic COSV5001, cosmic curated COSV50015, Variant assessed as somatic; moderate impact.
- T36I (p.Thr36Ile), cosmic curated COSV10874
- T36S (p.Thr36Ser), TOPMed rs1850985244
- M37I (p.Met37Ile), TOPMed rs1850984509
- M37K (p.Met37Lys), 1000Genomes rs531538376, ExAC rs531538376, TOPMed rs531538376, gnomAD rs531538376, REVEL 0.41, CADD 22.90
- M37T (p.Met37Thr), 1000Genomes rs531538376, ExAC rs531538376, TOPMed rs531538376, gnomAD rs531538376, REVEL 0.32, CADD 23.50
- M37V (p.Met37Val), gnomAD rs952524725, REVEL 0.27, CADD 23.30
- D38A (p.Asp38Ala), TOPMed rs1029936477, gnomAD rs1029936477, REVEL 0.27, CADD 24.70
- D38H (p.Asp38His), cosmic curated COSV10499
- V39A (p.Val39Ala), rs2497228455, ClinGen CA379798823, ClinVar RCV002796248, REVEL 0.20, CADD 26.50, Uncertain significance, not provided
- V39M (p.Val39Met), ExAC rs781491502, TOPMed rs781491502, gnomAD rs781491502, REVEL 0.12, CADD 25.30, Uncertain significance, not provided
- A40P (p.Ala40Pro), NCI-TCGA Cosmic COSV5002, cosmic curated COSV50026, Variant assessed as somatic; moderate impact.
- A40V (p.Ala40Val), NCI-TCGA TCGA novel, Ensembl rs1850983645, REVEL 0.04, CADD 18.90, Variant assessed as somatic; moderate impact.
- V41M (p.Val41Met), rs780439529, ClinGen CA5905159, ClinVar RCV001195265, ClinVar RCV001664744, REVEL 0.21, CADD 26.60, Conflicting interpretations, Inborn genetic diseases; Usher syndrome type 1C; not specified
- L42F (p.Leu42Phe), rs545856155, ClinGen CA5905158, ClinVar RCV002756618, 1000Genomes rs545856155, REVEL 0.08, CADD 23.90, Uncertain significance, not provided
- V43G (p.Val43Gly), rs1013399574, ClinGen CA218465440, ClinVar RCV001972910, Ensembl rs1013399574, AlphaMissense 0.87, MetaLR 0.15, Uncertain significance, not provided
- V43L (p.Val43Leu), rs145500807, cosmic curated COSV50021, ClinGen CA379798717, ClinVar RCV001341656, REVEL 0.18, CADD 24.20, Uncertain significance, not provided
- V43M (p.Val43Met), rs145500807, ClinGen CA142295, cosmic curated COSV50014, ClinVar RCV000041252, REVEL 0.22, CADD 24.40, Uncertain significance, not specified; not provided
- G44E (p.Gly44Glu), gnomAD rs1172593092
- D45A (p.Asp45Ala), gnomAD rs1592024029
- D45E (p.Asp45Glu), rs140319839, ClinGen CA5905156, ClinVar RCV002600073, ESP rs140319839, REVEL 0.26, CADD 24.50, Uncertain significance, not provided
- D45G (p.Asp45Gly), gnomAD rs1592024029, REVEL 0.45, CADD 29.60
- K47R (p.Lys47Arg), TOPMed rs1455042541
- K47T (p.Lys47Thr), rs1455042541, ClinGen CA379798567, ClinVar RCV004484407, AlphaMissense 0.18, MetaLR 0.08, Uncertain significance, Inborn genetic diseases
- L48M (p.Leu48Met), NCI-TCGA Cosmic COSV9914, cosmic curated COSV99142, Variant assessed as somatic; moderate impact.
- L48V (p.Leu48Val), rs374829758, ClinGen CA5905154, ClinVar RCV002284915, ESP rs374829758, REVEL 0.08, CADD 22.30, Uncertain significance, not provided
- V49L (p.Val49Leu), rs146817459, ClinGen CA5905153, ClinVar RCV002685621, ESP rs146817459, REVEL 0.17, CADD 22.70, Uncertain significance, not provided
- I50V (p.Ile50Val), rs1257461261, ClinGen CA379798484, ClinVar RCV001297923, gnomAD rs1257461261, REVEL 0.17, CADD 23.70, Uncertain significance, not provided
- N51H (p.Asn51His), Ensembl rs1850980698
- N51S (p.Asn51Ser), rs775363189, ClinGen CA5905152, ClinVar RCV000221329, ClinVar RCV001589139, REVEL 0.05, CADD 21.80, Uncertain significance, Usher syndrome type 1C; Usher syndrome type 1; Autosomal recessive nonsyndromic
- E52* (p.Glu52Ter), NCI-TCGA Cosmic COSV5003, Variant assessed as somatic; high impact.
- E52D (p.Glu52Asp), Ensembl rs1592023929
- E52K (p.Glu52Lys), NCI-TCGA Cosmic COSV5003, cosmic curated COSV50039, Ensembl rs1850980408, REVEL 0.23, CADD 25.00, Variant assessed as somatic; moderate impact.
- P53R (p.Pro53Arg), rs1000780029, ClinGen CA218465373, ClinVar RCV003277838, gnomAD rs1000780029, REVEL 0.53, CADD 28.60, Uncertain significance, Inborn genetic diseases
- P53S (p.Pro53Ser), cosmic curated COSV50014
- S54N (p.Ser54Asn), gnomAD rs1850979805, REVEL 0.09, CADD 18.60
- S54R (p.Ser54Arg), ExAC rs767509662, TOPMed rs767509662, gnomAD rs767509662, REVEL 0.07, CADD 22.90, Likely benign
- R55C (p.Arg55Cys), rs117171411, ClinGen CA5905150, ClinVar RCV001365640, ClinVar RCV001826045, REVEL 0.48, CADD 32.00, Uncertain significance, not provided
- R55H (p.Arg55His), rs1042393529, ClinGen CA218465335, cosmic curated COSV50046, ClinVar RCV000614227, REVEL 0.44, CADD 28.90, Uncertain significance, not specified; Usher syndrome type 1C
- R55S (p.Arg55Ser), 1000Genomes rs117171411, ESP rs117171411, ExAC rs117171411, TOPMed rs117171411, REVEL 0.27, CADD 24.90, Uncertain significance
- L56M (p.Leu56Met), ExAC rs774197490, gnomAD rs774197490, REVEL 0.19, CADD 25.10
- P57H (p.Pro57His), gnomAD rs1341678124, REVEL 0.39, CADD 28.80
- F59C (p.Phe59Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- D60G (p.Asp60Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- D60H (p.Asp60His), NCI-TCGA Cosmic COSV5003, cosmic curated COSV50030, Variant assessed as somatic; moderate impact.
- D60V (p.Asp60Val), TOPMed rs1850978124, gnomAD rs1850978124, REVEL 0.32, CADD 25.20
- I62T (p.Ile62Thr), TOPMed rs1306706999
- I62V (p.Ile62Val), ExAC rs776833569, gnomAD rs776833569
- R63G (p.Arg63Gly), ESP rs375741564, ExAC rs375741564, TOPMed rs375741564, gnomAD rs375741564, Uncertain significance
- R63Q (p.Arg63Gln), rs372497947, ClinGen CA243367, cosmic curated COSV99140, ClinVar RCV000177238, REVEL 0.73, CADD 28.90, Uncertain significance, Autosomal recessive nonsyndromic hearing loss 18A; Usher syndrome type 1C; Usher
- R63W (p.Arg63Trp), rs375741564, ClinGen CA5905144, cosmic curated COSV99142, ClinVar RCV000664634, REVEL 0.36, CADD 26.10, Uncertain significance, not provided
- P64L (p.Pro64Leu), rs758959670, ClinGen CA5905143, ClinVar RCV001866707, ExAC rs758959670, REVEL 0.30, CADD 23.30, Uncertain significance, not provided
- P64Q (p.Pro64Gln), ExAC rs758959670, gnomAD rs758959670, Uncertain significance
- P64S (p.Pro64Ser), cosmic curated COSV50014
- L65M (p.Leu65Met), TOPMed rs1850976270, REVEL 0.13, CADD 23.60
- L65P (p.Leu65Pro), rs1186965957, ClinGen CA379798133, ClinVar RCV002272826, TOPMed rs1186965957, REVEL 0.52, CADD 29.40, Uncertain significance, Usher syndrome type 1C
- I66S (p.Ile66Ser), ESP rs145040342, ExAC rs145040342, TOPMed rs145040342, gnomAD rs145040342, REVEL 0.47, CADD 29.50
- P67L (p.Pro67Leu), rs1850975781, ClinGen CA379798078, cosmic curated COSV50036, ClinVar RCV001106429, AlphaMissense 0.82, MetaLR 0.18, Uncertain significance, Usher syndrome type 1C
- L68M (p.Leu68Met), cosmic curated COSV10499
- H70N (p.His70Asn), cosmic curated COSV10499, NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- H70Q (p.His70Gln), rs1256576403, ClinGen CA379797978, ClinVar RCV003175320, TOPMed rs1256576403, REVEL 0.19, CADD 24.90, Uncertain significance, Inborn genetic diseases
- H70Y (p.His70Tyr), ExAC rs753527535, gnomAD rs753527535
- Q71K (p.Gln71Lys), gnomAD rs1193648847, REVEL 0.32, CADD 26.70
- V72E (p.Val72Glu), gnomAD rs1265464766, REVEL 0.48, CADD 28.40
- V72L (p.Val72Leu), ExAC rs763766845, TOPMed rs763766845, gnomAD rs763766845, REVEL 0.13, CADD 22.50, Uncertain significance
- V72M (p.Val72Met), rs763766845, ClinGen CA5905138, ClinVar RCV002585574, ExAC rs763766845, REVEL 0.26, CADD 24.10, Uncertain significance, not provided
- E73Q (p.Glu73Gln), TOPMed rs1182093939, gnomAD rs1182093939, REVEL 0.07, CADD 24.70
- D75E (p.Asp75Glu), 1000Genomes rs111033279, ESP rs111033279, ExAC rs111033279, TOPMed rs111033279, REVEL 0.20, CADD 24.60, Benign
- D75N (p.Asp75Asn), cosmic curated COSV10499, Ensembl rs868058857
- T78I (p.Thr78Ile), cosmic curated COSV50040, ExAC rs759581780, gnomAD rs759581780, REVEL 0.33, CADD 28.70
- T78N (p.Thr78Asn), ExAC rs759581780, gnomAD rs759581780, REVEL 0.20, CADD 27.40
- R80G (p.Arg80Gly), rs774005703, ClinGen CA218465227, ClinVar RCV000613861, ClinVar RCV001346255, REVEL 0.09, CADD 24.90, Uncertain significance, not provided; Inborn genetic diseases; not specified
- R80L (p.Arg80Leu), ESP rs148597739, ExAC rs148597739, TOPMed rs148597739, gnomAD rs148597739, Uncertain significance
- R80P (p.Arg80Pro), ESP rs148597739, ExAC rs148597739, TOPMed rs148597739, gnomAD rs148597739, REVEL 0.13, CADD 29.20, Uncertain significance
- R80Q (p.Arg80Gln), rs148597739, ClinGen CA5905133, ClinVar RCV001302460, ClinVar RCV001835453, REVEL 0.10, CADD 24.70, Uncertain significance, not provided
- R80W (p.Arg80Trp), rs774005703, ClinGen CA5905135, ClinVar RCV001307008, ClinVar RCV001830236, REVEL 0.25, CADD 32.00, Uncertain significance, not provided
- R81C (p.Arg81Cys), rs876658111, ClinGen CA10576848, cosmic curated COSV10720, ClinVar RCV000223556, REVEL 0.28, CADD 32.00, Uncertain significance, not specified; not provided
- R81H (p.Arg81His), ExAC rs776956839, gnomAD rs776956839, REVEL 0.14, CADD 26.40, Uncertain significance, Inborn genetic diseases
- R81L (p.Arg81Leu), NCI-TCGA Cosmic COSV5002, cosmic curated COSV50027, Variant assessed as somatic; moderate impact.
- S82C (p.Ser82Cys), rs769021971, ClinGen CA10576847, ClinVar RCV000215948, ClinVar RCV000671029, REVEL 0.42, CADD 29.50, Uncertain significance, not specified
- S82F (p.Ser82Phe), ExAC rs769021971, TOPMed rs769021971, gnomAD rs769021971, REVEL 0.43, CADD 29.90, Uncertain significance
- S82P (p.Ser82Pro), rs2133919543, ClinGen CA379797687, ClinVar RCV001906979, Ensembl rs2133919543, AlphaMissense 0.72, MetaLR 0.07, Uncertain significance, not provided
- R83G (p.Arg83Gly), gnomAD rs1422895060, REVEL 0.23, CADD 35.00
- R83K (p.Arg83Lys), NCI-TCGA Cosmic COSV9913, cosmic curated COSV99139, Variant assessed as somatic; moderate impact.
- E87K (p.Glu87Lys), TOPMed rs1335710937, gnomAD rs1335710937, REVEL 0.31, CADD 29.10
- V88G (p.Val88Gly), Ensembl rs1592022977
- V88M (p.Val88Met), NCI-TCGA Cosmic COSV9914, cosmic curated COSV99140, Variant assessed as somatic; moderate impact.
- R89C (p.Arg89Cys), rs764346200, ExAC rs764346200, gnomAD rs764346200, REVEL 0.31, AlphaMissense 0.35, Variant assessed as somatic; moderate impact.
- R89H (p.Arg89His), rs749647539, ClinGen CA5905110, ClinVar RCV000669302, ClinVar RCV001071473, REVEL 0.75, CADD 29.80, Uncertain significance, not specified; not provided
- L90P (p.Leu90Pro), NCI-TCGA Cosmic COSV5001, cosmic curated COSV50017, Variant assessed as somatic; moderate impact.
- D91G (p.Asp91Gly), rs2497224482, ClinGen CA379797340, ClinVar RCV003990306, Uncertain significance, Usher syndrome type 1C
- D91Y (p.Asp91Tyr), cosmic curated COSV50017, gnomAD rs1342634019, REVEL 0.27, CADD 27.90
- R92C (p.Arg92Cys), ExAC rs775407483, TOPMed rs775407483, gnomAD rs775407483, REVEL 0.59, CADD 32.00, Uncertain significance
- R92G (p.Arg92Gly), cosmic curated COSV10632, ExAC rs775407483, TOPMed rs775407483, gnomAD rs775407483, REVEL 0.57, CADD 29.00, Uncertain significance
- R92H (p.Arg92His), rs147954324, ClinGen CA5905108, cosmic curated COSV50024, ClinVar RCV000349369, REVEL 0.43, AlphaMissense 0.46, Uncertain significance, Inborn genetic diseases; not provided
- R92S (p.Arg92Ser), rs775407483, ClinGen CA379797328, ClinVar RCV002029031, ClinVar RCV005772329, REVEL 0.49, CADD 28.50, Uncertain significance, Inborn genetic diseases; not provided
- L93V (p.Leu93Val), Ensembl rs1850959463
- H94Q (p.His94Gln), 1000Genomes rs554615192, ExAC rs554615192, TOPMed rs554615192, gnomAD rs554615192, REVEL 0.13, CADD 18.10, Likely benign
- H94R (p.His94Arg), rs2497224342, ClinGen CA379797282, ClinVar RCV003025169, Uncertain significance, not provided
- H94Y (p.His94Tyr), gnomAD rs1850959183, REVEL 0.11, CADD 23.40
- P95A (p.Pro95Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- P95S (p.Pro95Ser), gnomAD rs1415557754
- P95T (p.Pro95Thr), gnomAD rs1415557754, REVEL 0.17, CADD 26.20
- E96* (p.Glu96Ter), rs769420899, NCI-TCGA Cosmic COSV5001, NCI-TCGA Cosmic COSV9914, cosmic curated COSV99140, AlphaMissense 0.31, MetaLR 0.09, Likely pathogenic
- E96K (p.Glu96Lys), rs769420899, NCI-TCGA Cosmic COSV5001, cosmic curated COSV50014, NCI-TCGA Cosmic COSV9914, REVEL 0.12, AlphaMissense 0.31, Uncertain significance, not provided
- G97D (p.Gly97Asp), TOPMed rs1850958048, REVEL 0.51, CADD 26.10
- G99C (p.Gly99Cys), rs370054635, ClinGen CA5905101, ClinVar RCV002038368, ClinVar RCV003355786, REVEL 0.88, CADD 26.90, Uncertain significance, Inborn genetic diseases; not provided
- G99D (p.Gly99Asp), cosmic curated COSV10452, REVEL 0.86, CADD 25.60
- G99S (p.Gly99Ser), rs370054635, ClinGen CA5905100, cosmic curated COSV10952, ClinVar RCV002997921, REVEL 0.89, CADD 26.00, Uncertain significance, Inborn genetic diseases
- R103C (p.Arg103Cys), rs397517880, ClinGen CA142371, cosmic curated COSV99140, ClinVar RCV000041289, REVEL 0.83, CADD 31.00, Conflicting interpretations, not provided; Usher syndrome type 1; Usher syndrome type 1C
- R103H (p.Arg103His), rs397514500, ClinGen CA261116, cosmic curated COSV50015, ClinVar RCV000032622, REVEL 0.58, CADD 27.70, Pathogenic/Likely pathogenic, not provided; Usher syndrome type 1; Usher syndrome type 1C
- R103L (p.Arg103Leu), rs397514500, NCI-TCGA Cosmic COSV5001, cosmic curated COSV50014, REVEL 0.55, AlphaMissense 0.11, Pathogenic
- R103P (p.Arg103Pro), rs397514500, ClinGen CA218464934, ClinVar RCV002632131, ExAC rs397514500, REVEL 0.69, AlphaMissense 0.11, Uncertain significance, not provided
- R103S (p.Arg103Ser), rs397517880, ClinGen CA379797139, ClinVar RCV001368100, 1000Genomes rs397517880, REVEL 0.41, CADD 27.50, Uncertain significance, not provided
- G104C (p.Gly104Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G104D (p.Gly104Asp), rs1317951509, ClinGen CA379797120, ClinVar RCV000669659, ClinVar RCV001004554, REVEL 0.90, CADD 25.80, Likely pathogenic, not provided; Usher syndrome type 1; Usher syndrome type 1C
- G104R (p.Gly104Arg), rs1387867750, ClinGen CA379797124, ClinVar RCV001733495, TOPMed rs1387867750, REVEL 0.82, CADD 26.40, Likely pathogenic, not provided
- G105A (p.Gly105Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G105D (p.Gly105Asp), rs999357481, TOPMed rs999357481, AlphaMissense 0.99, MetaLR 0.18, Variant assessed as somatic; moderate impact.
- L106V (p.Leu106Val), ExAC rs750240156, gnomAD rs750240156
- E107A (p.Glu107Ala), ExAC rs765184158, gnomAD rs765184158, REVEL 0.59, CADD 29.50
- E107K (p.Glu107Lys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G109A (p.Gly109Ala), TOPMed rs1320230679, gnomAD rs1320230679, Uncertain significance
Public USH1C analysis runs
- USH1C analysis run — USH1C (937 variants) — completed 2026-08-22