GIPC1
GIPC PDZ domain containing family member 1, the group of PDZ domain containing
Basic information
Region (hg38): 19:14477759-14496149
Previous symbols: [ "C19orf3", "RGS19IP1" ]
Links
Phenotypes
GenCC
Source:
- oculopharyngodistal myopathy (Supportive), mode of inheritance: AD
- oculopharyngodistal myopathy 2 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Oculopharyngodistal myopathy 2 | AD | 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 | Musculoskeletal | 32413282 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIPC1 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 | 1 | |||||
| missense | 27 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 27 | 3 | 0 |
Variants in GIPC1
This is a list of pathogenic ClinVar variants found in the GIPC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-14478420-T-C | not specified | Uncertain significance (Dec 21, 2022) | ||
| 19-14478427-C-T | not specified | Uncertain significance (May 04, 2023) | ||
| 19-14478692-G-A | not specified | Uncertain significance (Jun 21, 2021) | ||
| 19-14479437-C-T | not specified | Uncertain significance (May 30, 2023) | ||
| 19-14479438-G-A | not specified | Uncertain significance (Sep 22, 2022) | ||
| 19-14479447-G-A | not specified | Uncertain significance (Jan 08, 2024) | ||
| 19-14479461-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 19-14479468-T-G | not specified | Uncertain significance (Jul 27, 2022) | ||
| 19-14479489-C-T | not specified | Uncertain significance (Mar 27, 2023) | ||
| 19-14479503-G-A | Benign/Likely benign (Mar 01, 2023) | |||
| 19-14479504-C-T | not specified | Uncertain significance (Jun 01, 2023) | ||
| 19-14479515-C-T | not specified | Uncertain significance (Oct 16, 2023) | ||
| 19-14479522-T-C | not specified | Uncertain significance (May 08, 2024) | ||
| 19-14480316-C-A | not specified | Uncertain significance (May 25, 2023) | ||
| 19-14480446-T-G | not specified | Uncertain significance (Mar 19, 2024) | ||
| 19-14480458-G-C | not specified | Uncertain significance (Jan 22, 2024) | ||
| 19-14480484-C-T | Uncertain significance (Mar 01, 2017) | |||
| 19-14480618-T-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 19-14480646-C-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| 19-14480723-C-T | not specified | Uncertain significance (Dec 09, 2023) | ||
| 19-14480738-T-C | not specified | Uncertain significance (Nov 02, 2023) | ||
| 19-14480743-G-T | not specified | Uncertain significance (Aug 02, 2023) | ||
| 19-14480749-T-G | not specified | Uncertain significance (Jul 20, 2021) | ||
| 19-14482697-T-C | not specified | Likely benign (Jan 30, 2024) | ||
| 19-14482715-C-T | not specified | Uncertain significance (Jul 14, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GIPC1 | protein_coding | protein_coding | ENST00000393033 | 6 | 18373 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00831 | 0.938 | 125737 | 0 | 8 | 125745 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.542 | 196 | 219 | 0.897 | 0.0000149 | 2109 |
| Missense in Polyphen | 65 | 76.978 | 0.8444 | 852 | ||
| Synonymous | -1.64 | 120 | 99.2 | 1.21 | 0.00000724 | 716 |
| Loss of Function | 1.67 | 5 | 11.0 | 0.456 | 5.67e-7 | 131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000546 | 0.0000544 |
| Finnish | 0.0000949 | 0.0000924 |
| European (Non-Finnish) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.0000546 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000165 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in G protein-linked signaling.;
- Pathway
- VEGFA-VEGFR2 Signaling Pathway;Neurotrophic factor-mediated Trk receptor signaling;Syndecan-4-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.199
Intolerance Scores
- loftool
- 0.0983
- rvis_EVS
- 0.11
- rvis_percentile_EVS
- 61.73
Haploinsufficiency Scores
- pHI
- 0.421
- hipred
- Y
- hipred_score
- 0.628
- ghis
- 0.490
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.765
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gipc1
- Phenotype
- growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; renal/urinary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- gipc1
- Affected structure
- vascular lymphangioblast
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein targeting;G protein-coupled receptor signaling pathway;chemical synaptic transmission;glutamate secretion;positive regulation of transforming growth factor beta receptor signaling pathway;regulation of protein stability;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;positive regulation of cytokinesis;endothelial cell migration;regulation of synaptic plasticity;cellular response to interleukin-7;regulation of synaptic vesicle exocytosis
- Cellular component
- cytoplasm;cytosol;brush border;cell cortex;synaptic vesicle;vesicle membrane;membrane;endocytic vesicle;cytoplasmic vesicle;dendritic spine;dendritic shaft;extracellular exosome;Schaffer collateral - CA1 synapse;glutamatergic synapse
- Molecular function
- actin binding;signaling receptor binding;protein binding;myosin binding;PDZ domain binding;protein homodimerization activity;cadherin binding