IMPG2
Basic information
Region (hg38): 3:101222546-101320575
Links
Phenotypes
GenCC
Source:
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- adult-onset foveomacular vitelliform dystrophy (Supportive), mode of inheritance: AD
- retinitis pigmentosa 56 (Strong), mode of inheritance: AR
- retinitis pigmentosa 56 (Definitive), mode of inheritance: AR
- vitelliform macular dystrophy 5 (Definitive), mode of inheritance: AD
- vitelliform macular dystrophy 5 (Limited), mode of inheritance: Unknown
- inherited retinal dystrophy (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Macular dystrophy, vitelliform, 5; Retinitis pigmentosa 56 | AD/AR | General | 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 | 20673862; 25085631 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (45 variants)
- Retinal dystrophy (10 variants)
- Retinitis pigmentosa 56 (7 variants)
- Retinitis pigmentosa (5 variants)
- Autosomal recessive retinitis pigmentosa (2 variants)
- Vitelliform macular dystrophy 5 (2 variants)
- Macular dystrophy (1 variants)
- Vitelliform macular dystrophy 2 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMPG2 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 | 135 | 143 | ||||
missense | 418 | 428 | ||||
nonsense | 23 | 16 | 39 | |||
start loss | 0 | |||||
frameshift | 29 | 38 | ||||
inframe indel | 8 | |||||
splice donor/acceptor (+/-2bp) | 21 | 23 | ||||
splice region | 1 | 19 | 14 | 2 | 36 | |
non coding | 87 | 66 | 20 | 173 | ||
Total | 55 | 49 | 518 | 204 | 26 |
Highest pathogenic variant AF is 0.0000461
Variants in IMPG2
This is a list of pathogenic ClinVar variants found in the IMPG2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-101222595-T-C | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101222826-T-C | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101222848-A-C | Retinitis pigmentosa | Benign (Jan 13, 2018) | ||
3-101222861-C-G | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101222909-G-T | Retinitis Pigmentosa, Recessive | Uncertain significance (Jun 14, 2016) | ||
3-101222995-T-C | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223020-G-A | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223144-C-T | Retinitis pigmentosa | Uncertain significance (Jan 12, 2018) | ||
3-101223145-G-A | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223189-A-T | Retinitis pigmentosa | Benign (Jan 13, 2018) | ||
3-101223195-C-T | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223196-G-A | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223229-G-A | Retinitis pigmentosa | Uncertain significance (Jan 12, 2018) | ||
3-101223311-G-A | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223334-TAAAAC-T | Retinitis Pigmentosa, Recessive | Uncertain significance (Jun 14, 2016) | ||
3-101223345-A-C | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223350-G-A | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223350-G-T | Retinitis pigmentosa | Uncertain significance (Jan 12, 2018) | ||
3-101223370-T-C | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223455-G-A | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223502-C-T | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223682-G-C | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223734-G-T | Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
3-101223817-A-G | Retinitis pigmentosa | Uncertain significance (Jan 12, 2018) | ||
3-101223866-C-A | Retinitis pigmentosa | Uncertain significance (Jan 12, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IMPG2 | protein_coding | protein_coding | ENST00000193391 | 19 | 98015 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.75e-13 | 1.00 | 125682 | 0 | 66 | 125748 | 0.000262 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.207 | 641 | 626 | 1.02 | 0.0000312 | 8159 |
Missense in Polyphen | 110 | 137.93 | 0.79751 | 1937 | ||
Synonymous | -0.238 | 236 | 231 | 1.02 | 0.0000122 | 2372 |
Loss of Function | 3.27 | 30 | 56.5 | 0.531 | 0.00000285 | 727 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000451 | 0.000449 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000762 | 0.000761 |
Finnish | 0.0000925 | 0.0000924 |
European (Non-Finnish) | 0.000282 | 0.000281 |
Middle Eastern | 0.000762 | 0.000761 |
South Asian | 0.000229 | 0.000229 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Chondroitin sulfate- and hyaluronan-binding proteoglycan involved in the organization of interphotoreceptor matrix; may participate in the maturation and maintenance of the light- sensitive photoreceptor outer segment. Binds heparin. {ECO:0000269|PubMed:10702256}.;
- Disease
- DISEASE: Retinitis pigmentosa 56 (RP56) [MIM:613581]: 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:20673862}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Macular dystrophy, vitelliform, 5 (VMD5) [MIM:616152]: A form of macular dystrophy, a retinal disease in which various forms of deposits, pigmentary changes, and atrophic lesions are observed in the macula lutea. Vitelliform macular dystrophies are characterized by yellow, lipofuscin-containing deposits, usually localized at the center of the macula. VMD5 features include late- onset moderate visual impairment and preservation of retinal pigment epithelium reflectivity. {ECO:0000269|PubMed:20673862, ECO:0000269|PubMed:25085631}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.864
- rvis_EVS
- -0.84
- rvis_percentile_EVS
- 11.45
Haploinsufficiency Scores
- pHI
- 0.114
- hipred
- N
- hipred_score
- 0.251
- ghis
- 0.415
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.112
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Impg2
- Phenotype
Gene ontology
- Biological process
- visual perception
- Cellular component
- integral component of membrane;extracellular matrix;interphotoreceptor matrix;receptor complex
- Molecular function
- extracellular matrix structural constituent;hyaluronic acid binding;heparin binding