GIPC3

GIPC PDZ domain containing family member 3, the group of PDZ domain containing

Basic information

Region (hg38): 19:3585478-3593541

Previous symbols: [ "C19orf64", "DFNB72", "DFNB15" ]

Links

ENSG00000179855NCBI:126326OMIM:608792HGNC:18183Uniprot:Q8TF64AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Deafness, autosomal recessive 15ARAudiologic/OtolaryngologicEarly recognition and treatment of hearing impairment may improve outcomes, including speech and language developmentAudiologic/Otolaryngologic9286457; 9106521; 17690910; 21326233; 21660509; 23226338; 23510777

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GIPC3 gene.

  • not_provided (133 variants)
  • not_specified (46 variants)
  • Inborn_genetic_diseases (46 variants)
  • Autosomal_recessive_nonsyndromic_hearing_loss_15 (32 variants)
  • GIPC3-related_disorder (11 variants)
  • Rare_genetic_deafness (4 variants)
  • Hearing_impairment (4 variants)
  • Nonsyndromic_genetic_hearing_loss (1 variants)
  • Hearing_loss,_autosomal_recessive (1 variants)
  • Sensorineural_hearing_loss_disorder (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. These statistics are base on transcript: NM_000133261.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
39
clinvar
41
missense
5
clinvar
6
clinvar
93
clinvar
8
clinvar
112
nonsense
2
clinvar
1
clinvar
3
start loss
1
1
frameshift
3
clinvar
8
clinvar
11
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
1
clinvar
4
Total 11 18 95 48 0

Highest pathogenic variant AF is 0.000061688595

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GIPC3protein_codingprotein_codingENST00000322315 67989
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.009340.9441256630271256900.000107
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1771731800.9630.00001172007
Missense in Polyphen6066.5140.90207673
Synonymous-0.08197978.11.010.00000551649
Loss of Function1.73511.30.4445.72e-7138

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008730.0000873
Ashkenazi Jewish0.000.00
East Asian0.0001100.000109
Finnish0.00004620.0000462
European (Non-Finnish)0.0001430.000141
Middle Eastern0.0001100.000109
South Asian0.00009830.0000980
Other0.0003270.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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);