GIPC3
Basic information
Region (hg38): 19:3585478-3593541
Previous symbols: [ "C19orf64", "DFNB72", "DFNB15" ]
Links
Phenotypes
GenCC
Source:
- autosomal recessive nonsyndromic hearing loss 15 (Strong), mode of inheritance: AR
- autosomal recessive nonsyndromic hearing loss 15 (Strong), mode of inheritance: AR
- autosomal recessive nonsyndromic hearing loss 15 (Moderate), mode of inheritance: AR
- hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
- nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Deafness, autosomal recessive 15 | AR | Audiologic/Otolaryngologic | Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development | Audiologic/Otolaryngologic | 9286457; 9106521; 17690910; 21326233; 21660509; 23226338; 23510777 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (2 variants)
- Rare genetic deafness (2 variants)
- Hearing loss, autosomal recessive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIPC3 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 | 33 | 35 | ||||
| missense | 73 | 79 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 5 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | |||||
| splice region | 1 | 8 | 2 | 11 | ||
| non coding | 34 | 16 | 55 | |||
| Total | 4 | 9 | 79 | 69 | 17 |
Variants in GIPC3
This is a list of pathogenic ClinVar variants found in the GIPC3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GIPC3 | protein_coding | protein_coding | ENST00000322315 | 6 | 7989 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00934 | 0.944 | 125663 | 0 | 27 | 125690 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.177 | 173 | 180 | 0.963 | 0.0000117 | 2007 |
| Missense in Polyphen | 60 | 66.514 | 0.90207 | 673 | ||
| Synonymous | -0.0819 | 79 | 78.1 | 1.01 | 0.00000551 | 649 |
| Loss of Function | 1.73 | 5 | 11.3 | 0.444 | 5.72e-7 | 138 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000873 | 0.0000873 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000143 | 0.000141 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000983 | 0.0000980 |
| Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Required for postnatal maturation of the hair bundle and long-term survival of hair cells and spiral ganglion. {ECO:0000250}.;
- Disease
- DISEASE: Deafness, autosomal recessive, 15 (DFNB15) [MIM:601869]: A form of non-syndromic sensorineural hearing loss with prelingual onset. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:21326233, ECO:0000269|PubMed:21660509}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- 0.310
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.243
- hipred
- N
- hipred_score
- 0.384
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.180
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gipc3
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear 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);