SAG
S-antigen visual arrestin, the group of Classical arrestins
Basic information
Region (hg38): 2:233307815-233347055
Links
Phenotypes
GenCC
Source:
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- Oguchi disease (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Retinitis pigmentosa 96; Retinitis pigmentosa 47; Oguchi disease 1 | AD/AR | General | Manifesting 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 testing | Ophthalmologic | 7670478; 9565049; 21447990; 21494281; 21987685; 22665972; 28549094; 33047631 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (363 variants)
- Oguchi disease (54 variants)
- Retinitis pigmentosa (50 variants)
- not specified (10 variants)
- Retinal dystrophy (6 variants)
- Oguchi disease-1 (5 variants)
- Inborn genetic diseases (5 variants)
- Retinitis pigmentosa 47 (3 variants)
- Oguchi disease-1;Retinitis pigmentosa 47 (2 variants)
- Oguchi disease-2 (2 variants)
- Retinitis pigmentosa 47;Oguchi disease-1 (2 variants)
- Cone dystrophy (1 variants)
- SAG-Related Disorders (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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | 55 | 4 | 60 | ||
missense | 1 | 153 | 8 | 6 | 168 | |
nonsense | 6 | 6 | ||||
start loss | 0 | |||||
frameshift | 7 | 1 | 2 | 10 | ||
inframe indel | 1 | 1 | ||||
splice variant | 2 | 10 | 13 | 17 | 3 | 45 |
non coding | 8 | 42 | 40 | 90 | ||
Total | 16 | 11 | 178 | 122 | 53 |
Highest pathogenic variant AF is 0.000460
Variants in SAG
This is a list of pathogenic ClinVar variants found in the SAG region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-233307828-C-G | Oguchi disease • Retinitis pigmentosa | Conflicting interpretations of pathogenicity (Jan 13, 2018) | ||
2-233307982-G-A | Oguchi disease • Retinitis pigmentosa | Conflicting interpretations of pathogenicity (Jan 13, 2018) | ||
2-233309152-A-G | Oguchi disease • Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
2-233309179-G-A | Oguchi disease • Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
2-233309185-A-G | Uncertain significance (Nov 25, 2022) | |||
2-233309195-A-G | Likely benign (Jul 12, 2022) | |||
2-233309201-C-T | Likely benign (Jun 10, 2022) | |||
2-233309202-G-A | Uncertain significance (Aug 09, 2022) | |||
2-233309206-A-G | Uncertain significance (Jun 27, 2022) | |||
2-233309213-C-T | Uncertain significance (Jul 14, 2022) | |||
2-233309219-C-T | Likely benign (Oct 13, 2022) | |||
2-233309220-G-A | Retinitis pigmentosa • Oguchi disease | Conflicting interpretations of pathogenicity (Nov 01, 2022) | ||
2-233309224-C-T | Likely benign (Nov 01, 2022) | |||
2-233309225-G-A | Likely benign (Oct 01, 2022) | |||
2-233309241-A-G | Uncertain significance (May 10, 2022) | |||
2-233309253-C-T | Uncertain significance (Oct 03, 2022) | |||
2-233309254-G-A | Uncertain significance (Jul 30, 2022) | |||
2-233309256-G-C | Uncertain significance (Aug 23, 2022) | |||
2-233309256-GACAAATCGGTGAGTGGTGC-G | Likely pathogenic (Aug 28, 2021) | |||
2-233309263-C-A | Pathogenic (Nov 28, 2021) | |||
2-233309263-C-T | Uncertain significance (Nov 01, 2022) | |||
2-233309264-G-A | Cone dystrophy | Conflicting interpretations of pathogenicity (Aug 07, 2022) | ||
2-233309271-G-T | Oguchi disease • Retinitis pigmentosa | Conflicting interpretations of pathogenicity (Oct 10, 2022) | ||
2-233309276-A-C | Likely benign (Aug 20, 2022) | |||
2-233309280-G-A | Likely benign (Sep 12, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SAG | protein_coding | protein_coding | ENST00000409110 | 15 | 39240 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.49e-16 | 0.00634 | 124882 | 0 | 112 | 124994 | 0.000448 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.685 | 201 | 230 | 0.873 | 0.0000135 | 2613 |
Missense in Polyphen | 73 | 86.476 | 0.84417 | 1029 | ||
Synonymous | 1.04 | 81 | 93.9 | 0.863 | 0.00000602 | 767 |
Loss of Function | -0.101 | 24 | 23.5 | 1.02 | 0.00000123 | 281 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00197 | 0.00170 |
Ashkenazi Jewish | 0.000398 | 0.000397 |
East Asian | 0.000556 | 0.000552 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000271 | 0.000265 |
Middle Eastern | 0.000556 | 0.000552 |
South Asian | 0.00102 | 0.00101 |
Other | 0.000497 | 0.000493 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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