GIPC2

GIPC PDZ domain containing family member 2, the group of PDZ domain containing

Basic information

Region (hg38): 1:77979542-78138444

Links

ENSG00000137960 ∙ NCBI:54810 ∙ OMIM:619089 ∙ HGNC:18177 ∙ Uniprot:Q8TF65 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GIPC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIPC2 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in GIPC2

This is a list of pathogenic ClinVar variants found in the GIPC2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-77992848-C-T		DNAJB4-related disorder	Likely benign (Feb 27, 2024)
1-78005114-G-A		not specified	Uncertain significance (Oct 26, 2022)
1-78005164-A-C		not specified	Uncertain significance (Apr 28, 2023)
1-78005184-G-A		Congenital myopathy 21 with early respiratory failure	Pathogenic (Jul 16, 2024)
1-78005208-C-T		DNAJB4-related disorder	Uncertain significance (Jun 01, 2024)
1-78005267-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-78005291-A-G		Congenital myopathy 21 with early respiratory failure	Pathogenic (Jul 16, 2024)
1-78013065-G-C		not specified	Uncertain significance (Aug 12, 2022)
1-78013188-G-C		not specified	Uncertain significance (Aug 08, 2023)
1-78013224-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-78013277-G-C		not specified	Uncertain significance (Dec 01, 2022)
1-78013372-G-A		not specified	Uncertain significance (Sep 03, 2024)
1-78013384-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-78013542-A-G		not specified	Uncertain significance (Mar 30, 2024)
1-78013597-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-78016018-T-C		Congenital myopathy 21 with early respiratory failure	Pathogenic (Jul 16, 2024)
1-78016023-G-C		not specified	Uncertain significance (Feb 11, 2022)
1-78016041-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-78016089-A-T		Congenital myopathy 21 with early respiratory failure	Pathogenic (Jul 16, 2024)
1-78016095-G-A		not specified	Uncertain significance (Jun 05, 2024)
1-78016108-G-T		not specified	Uncertain significance (Jan 26, 2023)
1-78016134-C-G		not specified	Uncertain significance (Oct 29, 2024)
1-78016156-G-GT		DNAJB4-related disorder	Uncertain significance (Jun 01, 2024)
1-78046099-C-A		not specified	Uncertain significance (Apr 26, 2023)
1-78046141-C-T		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIPC2	protein_coding	protein_coding	ENST00000370759	6	158908

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.15e-9	0.0933	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.270	173	163	1.06	0.00000785	2014
Missense in Polyphen		53	51.64	1.0263		676
Synonymous	-0.00289	64	64.0	1.00	0.00000326	624
Loss of Function	-0.0327	13	12.9	1.01	6.03e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00166	0.00166
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.000278	0.000272
South Asian	0.000530	0.000523
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.563
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.300
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gipc2

Gene ontology

• Biological process: biological_process
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: molecular_function;protein binding;identical protein binding