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GeneBe

SAG

S-antigen visual arrestin, the group of Classical arrestins

Basic information

Region (hg38): 2:233307815-233347055

Links

ENSG00000130561NCBI:6295OMIM:181031HGNC:10521Uniprot:P10523AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • retinitis pigmentosa (Supportive), mode of inheritance: AD
  • Oguchi disease (Supportive), mode of inheritance: AR
  • Oguchi disease-1 (Definitive), mode of inheritance: AR
  • retinitis pigmentosa 47 (Definitive), mode of inheritance: AD
  • Oguchi disease-1 (Strong), mode of inheritance: AR
  • retinitis pigmentosa 96 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retinitis pigmentosa 96; Retinitis pigmentosa 47; Oguchi disease 1AD/ARGeneralManifesting heterozygotes have been described; Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic7670478; 9565049; 21447990; 21494281; 21987685; 22665972; 28549094; 33047631

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAG gene.

  • not provided (369 variants)
  • Oguchi disease (54 variants)
  • Retinitis pigmentosa (50 variants)
  • not specified (11 variants)
  • Inborn genetic diseases (8 variants)
  • Retinal dystrophy (6 variants)
  • Retinitis pigmentosa 47 (5 variants)
  • Oguchi disease-1 (5 variants)
  • Oguchi disease-1;Retinitis pigmentosa 47 (4 variants)
  • Oguchi disease-2 (2 variants)
  • SAG-Related Disorders (1 variants)
  • Cone dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAG gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
2
clinvar
48
clinvar
4
clinvar
54
missense
1
clinvar
157
clinvar
1
clinvar
3
clinvar
162
nonsense
6
clinvar
6
start loss
0
frameshift
7
clinvar
2
clinvar
9
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
2
clinvar
11
clinvar
1
clinvar
14
splice region
11
13
2
26
non coding
9
clinvar
44
clinvar
41
clinvar
94
Total 16 11 172 93 48

Highest pathogenic variant AF is 0.000460

Variants in SAG

This is a list of pathogenic ClinVar variants found in the SAG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
2-233307828-C-G Oguchi disease • Retinitis pigmentosa Conflicting classifications of pathogenicity (Jan 13, 2018)335064
2-233307982-G-A Retinitis pigmentosa • Oguchi disease Conflicting classifications of pathogenicity (Jan 13, 2018)896657
2-233309152-A-G Oguchi disease • Retinitis pigmentosa Uncertain significance (Jan 13, 2018)896658
2-233309179-G-A Oguchi disease • Retinitis pigmentosa Uncertain significance (Jan 13, 2018)335065
2-233309185-A-G Uncertain significance (Nov 25, 2022)2503179
2-233309194-C-T Uncertain significance (Jan 18, 2023)3008843
2-233309195-A-G Likely benign (Dec 20, 2023)1157265
2-233309201-C-T Retinal dystrophy Conflicting classifications of pathogenicity (Oct 01, 2023)1908380
2-233309202-G-A Uncertain significance (Aug 08, 2023)958764
2-233309206-A-G Uncertain significance (Jul 12, 2023)1017595
2-233309208-A-C Uncertain significance (Jul 20, 2023)2745571
2-233309213-C-T Uncertain significance (Jul 14, 2022)2017019
2-233309219-C-T Likely benign (Oct 13, 2022)1948212
2-233309220-G-A Retinitis pigmentosa • Oguchi disease • SAG-related disorder Conflicting classifications of pathogenicity (Jan 19, 2024)791237
2-233309224-C-T Likely benign (Nov 10, 2023)1088116
2-233309225-G-A Retinal dystrophy Conflicting classifications of pathogenicity (Oct 01, 2023)1924889
2-233309241-A-G Uncertain significance (May 10, 2022)1381222
2-233309253-C-T Uncertain significance (Dec 22, 2023)1015446
2-233309254-G-A Uncertain significance (Nov 17, 2023)1450481
2-233309255-G-A Likely benign (Jan 12, 2023)2988691
2-233309256-G-C Uncertain significance (Aug 23, 2022)2064144
2-233309256-GACAAATCGGTGAGTGGTGC-G Likely pathogenic (Nov 07, 2022)1511520
2-233309263-C-A Pathogenic (Nov 28, 2021)1452228
2-233309263-C-T Uncertain significance (Nov 19, 2023)972665
2-233309264-G-A Cone dystrophy Conflicting classifications of pathogenicity (Aug 07, 2022)813236

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAGprotein_codingprotein_codingENST00000409110 1539240
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.49e-160.0063412488201121249940.000448
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6852012300.8730.00001352613
Missense in Polyphen7386.4760.844171029
Synonymous1.048193.90.8630.00000602767
Loss of Function-0.1012423.51.020.00000123281

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001970.00170
Ashkenazi Jewish0.0003980.000397
East Asian0.0005560.000552
Finnish0.000.00
European (Non-Finnish)0.0002710.000265
Middle Eastern0.0005560.000552
South Asian0.001020.00101
Other0.0004970.000493

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds to photoactivated, phosphorylated RHO and terminates RHO signaling via G-proteins by competing with G- proteins for the same binding site on RHO (By similarity). May play a role in preventing light-dependent degeneration of retinal photoreceptor cells (PubMed:9565049). {ECO:0000250|UniProtKB:P08168, ECO:0000305|PubMed:9565049}.;
Disease
DISEASE: Night blindness, congenital stationary, Oguchi type 1 (CSNBO1) [MIM:258100]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. Congenital stationary night blindness Oguchi type is an autosomal recessive form associated with fundus discoloration and abnormally slow dark adaptation. {ECO:0000269|PubMed:7670478}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 47 (RP47) [MIM:613758]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:9565049}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Phototransduction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Visual signal transduction: Rods;G alpha (i) signalling events;Activation of the phototransduction cascade;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.463

Intolerance Scores

loftool
0.882
rvis_EVS
0.29
rvis_percentile_EVS
71.57

Haploinsufficiency Scores

pHI
0.248
hipred
N
hipred_score
0.331
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.591

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sag
Phenotype
vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype;

Gene ontology

Biological process
cell surface receptor signaling pathway;rhodopsin mediated signaling pathway;regulation of rhodopsin mediated signaling pathway;negative regulation of phosphoprotein phosphatase activity
Cellular component
photoreceptor outer segment;photoreceptor inner segment;cytosol;membrane
Molecular function
opsin binding;protein phosphatase inhibitor activity;phosphoprotein binding