GNAT1 (P11488) variants and mutations
GNAT1 (also known as P11488) is a human protein-coding gene encoding a guanine nucleotide-binding protein G(t) subunit alpha-1 protein. It transduces the light-activated rhodopsin signal in rod photoreceptors, activating phosphodiesterase and lowering cGMP to initiate visual responses. Pathogenic variants can cause congenital stationary night blindness or autosomal dominant rod-cone degeneration. This analysis covers 719 GNAT1 variants and mutations. Of these, 78% have computational variant effect predictions. Disease context includes congenital stationary night blindness autosomal dominant 3, congenital stationary night blindness, and congenital stationary night blindness 1G. Example GNAT1 variants include M1?, M1I, and M1V.
Variant analysis overview
- Gene: GNAT1
- Protein: P11488
- UniProt accession: P11488
- Organism: Homo sapiens
- Variants analyzed: 719
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 514 unspecified-consequence records; 102 synonymous variants; 76 missense variants; 17 frameshift variants; 3 in-frame deletions; 2 stop-gained variants; 3 splice-region variants; 3 substitution
- Prediction scores: 560 variants have prediction scores (78% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: congenital stationary night blindness autosomal dominant 3, congenital stationary night blindness, congenital stationary night blindness 1G, inherited retinal dystrophy, retinitis pigmentosa, Cone rod dystrophy, cone-rod dystrophy, Rod-cone dystrophy, retinal degeneration, Retinal dystrophy, neurodegenerative disease, hereditary disease.
Protein structure and variant hotspots
- Protein features: 1 domains; 19 binding sites; 3 post-translational modification sites.
- Structural context: 652 variants have structural context.
- 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 GNAT1 variants
Examples include M1?, M1I, M1V, G2V, G2G, A3T, A3D, A3V. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, cosmic curated COSV99137
- M1I (p.Met1Ile), rs753375778, ClinGen CA2412417, ClinVar RCV001348235, MetaLR 0.77, MetaSVM 0.67, Uncertain significance, not provided
- M1V (p.Met1Val), rs763736641, ClinGen CA2412416, ClinVar RCV001968871, MetaLR 0.75, MetaSVM 0.65, Uncertain significance, not provided
- G2V (p.Gly2Val), TOPMed rs1420138504, gnomAD rs1420138504, REVEL 0.80, CADD 26.70
- G2G (p.Gly2Gly), rs1328995578, gnomAD 3-50191731-G-A, CADD 11.90
- A3T (p.Ala3Thr), rs1266812415, ClinGen CA352908589, cosmic curated COSV99137, ClinVar RCV002001578, REVEL 0.45, CADD 23.80, Uncertain significance, not provided
- A3D (p.Ala3Asp), gnomAD 3-50191733-C-A, REVEL 0.56, CADD 23.40
- A3V (p.Ala3Val), gnomAD 3-50191733-C-T, REVEL 0.45, CADD 23.40
- A3A (p.Ala3Ala), gnomAD 3-50191734-T-C, CADD 13.20
- G4R (p.Gly4Arg), rs1699413898, ClinGen CA352908606, ClinVar RCV001867666, Ensembl rs1699413898, REVEL 0.57, CADD 23.10, Uncertain significance, not provided
- G4W (p.Gly4Trp), Ensembl rs1699413898, REVEL 0.67, CADD 29.90, Uncertain significance
- A5P (p.Ala5Pro), gnomAD 3-50191734-TG-T, CADD 28.00
- A5T (p.Ala5Thr), gnomAD 3-50191738-G-A, REVEL 0.36, CADD 23.80
- A5A (p.Ala5Ala), rs376502535, gnomAD 3-50191740-C-T, CADD 13.80
- S6G (p.Ser6Gly), rs780667765, ClinGen CA2412419, ClinVar RCV001317593, ExAC rs780667765, REVEL 0.73, CADD 26.60, Uncertain significance, not provided
- S6R (p.Ser6Arg), TOPMed rs1459356965, gnomAD rs1459356965, REVEL 0.55, CADD 16.00
- S6V (p.Ser6Val), gnomAD 3-50191738-GC-G, CADD 25.70
- A7V (p.Ala7Val), rs1293986442, NCI-TCGA Cosmic COSV5002, cosmic curated COSV50029, gnomAD rs1293986442, AlphaMissense 0.10, MetaLR 0.52, Variant assessed as somatic; moderate impact.
- E8D (p.Glu8Asp), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- E8K (p.Glu8Lys), cosmic curated COSV10498
- E8Q (p.Glu8Gln), gnomAD rs1384503071, REVEL 0.58, CADD 24.90
- E9A (p.Glu9Ala), Ensembl rs1575415985
- E9D (p.Glu9Asp), cosmic curated COSV10437
- E9K (p.Glu9Lys), cosmic curated COSV10581, REVEL 0.42, CADD 23.00
- E9del (p.Glu9del), rs398124522, gnomAD 3-50191746-TGAG-T, CADD 21.60
- K10E (p.Lys10Glu), gnomAD 3-50191753-A-G, REVEL 0.48, CADD 24.60
- K10K (p.Lys10Lys), rs747406154, gnomAD 3-50191755-G-A, CADD 11.30
- K10N (p.Lys10Asn), gnomAD 3-50191755-G-T, REVEL 0.55, CADD 24.80
- H11Y (p.His11Tyr), gnomAD rs1377171417, REVEL 0.43, CADD 23.20
- H11H (p.His11His), rs1019065205, gnomAD 3-50191758-C-T, CADD 9.25
- S12P (p.Ser12Pro), gnomAD 3-50191759-T-C, REVEL 0.83, CADD 27.10
- R13K (p.Arg13Lys), rs201006405, ClinGen CA2412421, ClinVar RCV000299430, ClinVar RCV001412336, REVEL 0.23, CADD 16.60, Benign/Likely benign, not provided; Congenital stationary night blindness autosomal dominant 3
- R13S (p.Arg13Ser), cosmic curated COSV50031
- R13R (p.Arg13Arg), rs201955783, gnomAD 3-50191764-G-A, CADD 11.40
- E14D (p.Glu14Asp), ExAC rs748389570, TOPMed rs748389570, gnomAD rs748389570, REVEL 0.50, CADD 23.60, Uncertain significance, not provided
- E14K (p.Glu14Lys), NCI-TCGA Cosmic COSV5002, cosmic curated COSV50029, Variant assessed as somatic; moderate impact.
- E14E (p.Glu14Glu), rs748389570, gnomAD 3-50191767-G-A, CADD 9.69
- L15L (p.Leu15Leu), gnomAD 3-50191770-G-T, CADD 10.80
- E16* (p.Glu16Ter), cosmic curated COSV10498
- E16G (p.Glu16Gly), ExAC rs770031393, gnomAD rs770031393, REVEL 0.88, CADD 31.00
- E16K (p.Glu16Lys), cosmic curated COSV10629
- E16Q (p.Glu16Gln), gnomAD 3-50191771-G-C, REVEL 0.79, CADD 26.70
- K17N (p.Lys17Asn), TOPMed rs1699414664
- K17R (p.Lys17Arg), cosmic curated COSV50029
- K18S (p.Lys18Ser), rs753761683, gnomAD 3-50191775-AG-A, CADD 27.30
- L19P (p.Leu19Pro), gnomAD 3-50191781-T-C, REVEL 0.92, CADD 28.60
- L19L (p.Leu19Leu), rs777848586, gnomAD 3-50191782-G-A, CADD 10.10
- K20E (p.Lys20Glu), rs1699414848, ClinGen CA352908838, ClinVar RCV003050124, Ensembl rs1699414848, REVEL 0.48, CADD 22.80, Uncertain significance, not provided
- E21K (p.Glu21Lys), cosmic curated COSV50032
- E21E (p.Glu21Glu), gnomAD 3-50191788-G-A, CADD 5.71
- D22D (p.Asp22Asp), rs367565550, gnomAD 3-50191791-C-T, CADD 7.74
- A23D (p.Ala23Asp), gnomAD rs1177827474, REVEL 0.69, CADD 23.70
- A23S (p.Ala23Ser), TOPMed rs1053549443, gnomAD rs1053549443, REVEL 0.49, CADD 23.80, Uncertain significance
- A23T (p.Ala23Thr), rs1053549443, ClinGen CA74598344, ClinVar RCV003877871, TOPMed rs1053549443, REVEL 0.56, CADD 24.70, Uncertain significance, not provided
- E24* (p.Glu24Ter), cosmic curated COSV10797
- K25N (p.Lys25Asn), NCI-TCGA Cosmic COSV9913, cosmic curated COSV99137, TOPMed rs1378270615, gnomAD rs1378270615, Variant assessed as somatic; moderate impact.
- K25R (p.Lys25Arg), Ensembl rs1575416010
- K25K (p.Lys25Lys), rs1378270615, gnomAD 3-50191800-G-A, CADD 11.10
- D26E (p.Asp26Glu), gnomAD rs1425289444, REVEL 0.31, CADD 6.76
- D26G (p.Asp26Gly), cosmic curated COSV50040
- D26L (p.Asp26Leu), gnomAD 3-50191799-AGGAT-, CADD 29.30
- A27T (p.Ala27Thr), rs1161256318, TOPMed rs1161256318, gnomAD rs1161256318, REVEL 0.64, CADD 24.50, Variant assessed as somatic; moderate impact.
- A27V (p.Ala27Val), gnomAD rs1165407105, REVEL 0.60, CADD 23.90
- A27A (p.Ala27Ala), rs201912686, gnomAD 3-50191806-T-C, CADD 10.40
- R28* (p.Arg28Ter), rs774214573, ClinGen CA2412432, NCI-TCGA Cosmic COSV5003, cosmic curated COSV50031, CADD 35.00, Likely pathogenic
- R28L (p.Arg28Leu), rs149936603, ClinGen CA352908988, ClinVar RCV003713247, AlphaMissense 0.19, MetaLR 0.45, Uncertain significance, not provided
- R28P (p.Arg28Pro), 1000Genomes rs149936603, ESP rs149936603, ExAC rs149936603, TOPMed rs149936603, REVEL 0.73, AlphaMissense 0.19, Benign
- R28Q (p.Arg28Gln), rs149936603, ClinGen CA2412433, ClinVar RCV000259457, ClinVar RCV001437241, REVEL 0.48, AlphaMissense 0.19, Conflicting interpretations, not provided; Congenital stationary night blindness autosomal dominant 3
- R28R (p.Arg28Arg), rs774214573, gnomAD 3-50191807-C-A, CADD 13.30
- T29A (p.Thr29Ala), gnomAD rs1400630067, REVEL 0.64, CADD 24.00
- T29I (p.Thr29Ile), gnomAD 3-50191811-C-T, REVEL 0.68, CADD 23.50
- T29T (p.Thr29Thr), rs775324794, gnomAD 3-50191812-C-T, CADD 6.53
- V30L (p.Val30Leu), ESP rs145040990, ExAC rs145040990, TOPMed rs145040990, gnomAD rs145040990, REVEL 0.74, CADD 24.40, Uncertain significance, Inborn genetic diseases
- V30M (p.Val30Met), rs145040990, ClinGen CA2412436, cosmic curated COSV10452, ClinVar RCV001878192, REVEL 0.85, CADD 29.10, Uncertain significance, not provided
- V30* (p.Val30Ter), gnomAD 3-50191810-AC-A, CADD 25.40
- K31N (p.Lys31Asn), gnomAD 3-50191818-G-C, REVEL 0.64, CADD 23.00
- L32L (p.Leu32Leu), rs1371671656, gnomAD 3-50191821-G-A, CADD 11.30
- L33L (p.Leu33Leu), gnomAD 3-50191822-C-T, CADD 12.70
- L34H (p.Leu34His), rs2109137515, ClinGen CA352909093, ClinVar RCV002025294, Ensembl rs2109137515, AlphaMissense 1.00, MetaLR 0.73, Uncertain significance, not provided
- L34R (p.Leu34Arg), gnomAD 3-50191826-T-G, REVEL 0.90, CADD 29.90
- L34L (p.Leu34Leu), rs1699415988, gnomAD 3-50191827-T-G, CADD 11.80
- L35L (p.Leu35Leu), gnomAD 3-50191828-C-T, CADD 12.40
- G36C (p.Gly36Cys), cosmic curated COSV50033
- G36D (p.Gly36Asp), rs772024349, ClinGen CA2412452, ClinVar RCV000787836, ClinVar RCV001370367, REVEL 0.95, CADD 32.00, Uncertain significance, not provided
- G36S (p.Gly36Ser), TOPMed rs1487464362, gnomAD rs1487464362, REVEL 0.99, CADD 35.00
- A37A (p.Ala37Ala), rs1195798989, gnomAD 3-50193137-C-T, CADD 2.05
- G38D (p.Gly38Asp), rs104893740, ClinGen CA126053, ClinVar RCV000017277, UniProt VAR 009279, REVEL 0.78, CADD 27.20, Pathogenic, Congenital stationary night blindness autosomal dominant 3
- G38R (p.Gly38Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact., in CSNBAD3
- G38S (p.Gly38Ser), gnomAD rs1347967126, REVEL 0.72, CADD 27.40
- E39D (p.Glu39Asp), rs34797487, ClinGen CA352911902, ClinVar RCV001307134, 1000Genomes rs34797487, REVEL 0.42, CADD 23.50, Uncertain significance, not provided
- E39K (p.Glu39Lys), gnomAD 3-50193141-G-A, REVEL 0.72, CADD 32.00
- E39E (p.Glu39Glu), rs34797487, gnomAD 3-50193143-G-A, CADD 9.61
- S40P (p.Ser40Pro), Ensembl rs1575416566
- G41A (p.Gly41Ala), Ensembl rs1699439597
- G41W (p.Gly41Trp), ExAC rs768429545
- G41G (p.Gly41Gly), gnomAD 3-50193149-G-A, CADD 9.30
- K42E (p.Lys42Glu), TOPMed rs1699439647, gnomAD rs1699439647, REVEL 0.86, CADD 31.00, Likely pathogenic, Congenital stationary night blindness 1C
- K42N (p.Lys42Asn), ExAC rs776367777, TOPMed rs776367777, gnomAD rs776367777, REVEL 0.74, CADD 25.40
- K42* (p.Lys42Ter), gnomAD 3-50193150-A-T, CADD 41.00
- K42K (p.Lys42Lys), rs776367777, gnomAD 3-50193152-G-A, CADD 11.90
- S43N (p.Ser43Asn), cosmic curated COSV10437
- S43I (p.Ser43Ile), gnomAD 3-50193154-G-T, REVEL 0.89, CADD 27.40
- S43S (p.Ser43Ser), gnomAD 3-50193155-C-T, CADD 13.40
- T44P (p.Thr44Pro), Ensembl rs1575416575
- T44S (p.Thr44Ser), rs2546143918, ClinGen CA352912062, ClinVar RCV002295206, Uncertain significance, not provided
- T44T (p.Thr44Thr), gnomAD 3-50193158-C-G, CADD 11.80
- I45I (p.Ile45Ile), gnomAD 3-50193161-C-A, CADD 13.20
- I45M (p.Ile45Met), gnomAD 3-50193161-C-G, REVEL 0.62, CADD 22.50
- V46I (p.Val46Ile), rs764910362, ClinGen CA2412457, ClinVar RCV002020824, ExAC rs764910362, AlphaMissense 0.40, MetaLR 0.50, Uncertain significance, not provided
- K47N (p.Lys47Asn), cosmic curated COSV99027
- K47Q (p.Lys47Gln), NCI-TCGA Cosmic COSV5002, cosmic curated COSV50028, Variant assessed as somatic; moderate impact.
- Q48E (p.Gln48Glu), rs749921670, ClinGen CA2412458, ClinVar RCV001910851, ClinVar RCV004988861, REVEL 0.85, CADD 24.60, Uncertain significance, not provided; Inborn genetic diseases
- Q48* (p.Gln48Ter), gnomAD 3-50193168-C-T, CADD 37.00
- Q48Q (p.Gln48Gln), gnomAD 3-50193170-G-A, CADD 12.70
- M49I (p.Met49Ile), Ensembl rs1559746052
- M49V (p.Met49Val), TOPMed rs1466539542
- K50E (p.Lys50Glu), gnomAD 3-50193174-A-G, REVEL 0.82, CADD 33.00
- K50R (p.Lys50Arg), gnomAD 3-50193175-A-G, REVEL 0.42, CADD 23.10
- K50K (p.Lys50Lys), gnomAD 3-50193265-G-A, CADD 16.40
- I51D (p.Ile51Asp), gnomAD 3-50193264-G-GA, CADD 37.00
- I52Y (p.Ile52Tyr), gnomAD 3-50193267-T-TC, CADD 28.90
- I52T (p.Ile52Thr), gnomAD 3-50193269-ATC-A, CADD 28.50
- I52I (p.Ile52Ile), gnomAD 3-50193271-C-A, CADD 11.30
- H53R (p.His53Arg), TOPMed rs1699441764, REVEL 0.95, CADD 26.30
- H53H (p.His53His), gnomAD 3-50193274-C-T, CADD 11.10
- Q54* (p.Gln54Ter), Ensembl rs778486199
- Q54X, rs778486199, []
- D55E (p.Asp55Glu), ExAC rs776566245, TOPMed rs776566245, gnomAD rs776566245, REVEL 0.28, CADD 7.58, Likely benign
- D55Y (p.Asp55Tyr), rs1041904269, ClinGen CA74601055, ClinVar RCV001305259, ClinVar RCV006372496, REVEL 0.81, CADD 29.30, Uncertain significance, Inborn genetic diseases; not provided
- D55N (p.Asp55Asn), gnomAD 3-50193278-G-A, REVEL 0.36, CADD 23.10
- D55D (p.Asp55Asp), rs776566245, gnomAD 3-50193280-C-T, CADD 5.61
- G56G (p.Gly56Gly), rs747846195, gnomAD 3-50193283-G-C, CADD 11.00
- Y57* (p.Tyr57Ter), rs190126440, ClinGen CA74601059, ClinVar RCV003820706, 1000Genomes rs190126440, CADD 34.00, Pathogenic
- S58* (p.Ser58Ter), cosmic curated COSV99137
- S58T (p.Ser58Thr), gnomAD 3-50193287-T-A, REVEL 0.15, CADD 21.40
- S58S (p.Ser58Ser), rs772624047, gnomAD 3-50193289-G-T, CADD 3.37
- L59P (p.Leu59Pro), rs2546144237, ClinGen CA352912760, ClinVar RCV003027430, REVEL 0.35, CADD 22.90, Uncertain significance, not provided
- E60K (p.Glu60Lys), TOPMed rs1242103172, gnomAD rs1242103172, REVEL 0.45, CADD 25.80, Uncertain significance, not provided
- E60Q (p.Glu60Gln), TOPMed rs1242103172, gnomAD rs1242103172, REVEL 0.18, CADD 23.10
- E61D (p.Glu61Asp), gnomAD 3-50193298-G-C, REVEL 0.24, CADD 23.00
- C62F (p.Cys62Phe), cosmic curated COSV10951
- C62C (p.Cys62Cys), rs1309682929, gnomAD 3-50193301-C-T, CADD 13.10
- L63V (p.Leu63Val), Ensembl rs1699442559
- L63F (p.Leu63Phe), gnomAD 3-50193302-C-T, REVEL 0.55, CADD 23.30
- E64Q (p.Glu64Gln), NCI-TCGA Cosmic COSV9913, cosmic curated COSV99137, Variant assessed as somatic; moderate impact.
- E64K (p.Glu64Lys), gnomAD 3-50193305-G-A, REVEL 0.78, CADD 25.60
- E64G (p.Glu64Gly), gnomAD 3-50193306-A-G, REVEL 0.81, CADD 25.70
- F65L (p.Phe65Leu), gnomAD rs1352647422, REVEL 0.82, CADD 24.90
- I66L (p.Ile66Leu), gnomAD 3-50193311-A-C, REVEL 0.50, CADD 22.60
- I66I (p.Ile66Ile), gnomAD 3-50193313-C-T, CADD 6.17
- A67T (p.Ala67Thr), cosmic curated COSV10872, REVEL 0.25, CADD 22.20
- A67A (p.Ala67Ala), gnomAD 3-50193316-C-T, CADD 14.70
- I68F (p.Ile68Phe), cosmic curated COSV10437
- I68V (p.Ile68Val), gnomAD 3-50193317-A-G, REVEL 0.37, CADD 18.40
- I68T (p.Ile68Thr), gnomAD 3-50193318-T-C, REVEL 0.88, CADD 26.30
- I68N (p.Ile68Asn), gnomAD 3-50193318-T-A, REVEL 0.91, CADD 28.70
- I68I (p.Ile68Ile), rs1205473151, gnomAD 3-50193319-C-T, CADD 13.80
- I69N (p.Ile69Asn), gnomAD 3-50193321-T-A, REVEL 0.71, CADD 29.00
- Y70* (p.Tyr70Ter), rs762489106, ClinGen CA2412481, ClinVar RCV003039918, ExAC rs762489106, CADD 32.00, Pathogenic
- Y70S (p.Tyr70Ser), rs2546144317, ClinGen CA352913256, ClinVar RCV002861498, Uncertain significance, not provided
- Y70C (p.Tyr70Cys), gnomAD 3-50193324-A-G, REVEL 0.94, CADD 28.40
- Y70Y (p.Tyr70Tyr), rs762489106, gnomAD 3-50193325-C-T, CADD 6.75
- G71C (p.Gly71Cys), rs767935708, ClinGen CA2412482, ClinVar RCV001373234, ClinVar RCV004815488, REVEL 0.65, CADD 26.40, Uncertain significance, not provided
- G71D (p.Gly71Asp), NCI-TCGA Cosmic COSV9913, cosmic curated COSV99138, REVEL 0.68, CADD 26.90, Variant assessed as somatic; moderate impact.
- G71S (p.Gly71Ser), ExAC rs767935708, gnomAD rs767935708, REVEL 0.37, CADD 18.60, Uncertain significance
- G71G (p.Gly71Gly), rs1451684911, gnomAD 3-50193328-C-G, CADD 11.40
- N72H (p.Asn72His), ExAC rs776116147, gnomAD rs776116147
- N72N (p.Asn72Asn), gnomAD 3-50193331-C-T, CADD 10.70
- T73K (p.Thr73Lys), TOPMed rs1236654107, Uncertain significance
- T73M (p.Thr73Met), rs1236654107, ClinGen CA352913370, cosmic curated COSV10437, ClinVar RCV001209348, REVEL 0.75, CADD 23.70, Uncertain significance, not provided
- T73A (p.Thr73Ala), gnomAD 3-50193332-A-G, REVEL 0.80, CADD 22.80
- T73T (p.Thr73Thr), gnomAD 3-50193334-G-A, CADD 9.28
- Q75* (p.Gln75Ter), Ensembl rs1699443183
- Q75R (p.Gln75Arg), NCI-TCGA Cosmic COSV5003, cosmic curated COSV50032, Variant assessed as somatic; moderate impact.
- Q75Q (p.Gln75Gln), rs761142046, gnomAD 3-50193340-G-A, CADD 11.90
- S76S (p.Ser76Ser), gnomAD 3-50193343-C-T, CADD 14.00
- I77F (p.Ile77Phe), rs764511104, ClinGen CA2412485, ClinVar RCV001961109, ExAC rs764511104, REVEL 0.80, CADD 23.10, Uncertain significance, not provided
- I77M (p.Ile77Met), rs754189877, ClinGen CA2412486, ClinVar RCV001314060, ClinVar RCV004815339, REVEL 0.28, CADD 13.70, Uncertain significance, Inborn genetic diseases; not provided
- I77L (p.Ile77Leu), gnomAD 3-50193344-A-C, REVEL 0.38, CADD 22.20
- I77I (p.Ile77Ile), rs754189877, gnomAD 3-50193346-C-T, CADD 13.20
Public GNAT1 analysis runs
- GNAT1 analysis run — GNAT1 (719 variants) — completed 2026-08-22