GCA

grancalcin, the group of EF-hand domain containing

Basic information

Region (hg38): 2:162318839-162371595

Links

ENSG00000115271 ∙ NCBI:25801 ∙ OMIM:607030 ∙ HGNC:15990 ∙ Uniprot:P28676 ∙ 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 GCA gene.

Variants pathogenicity by type

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

Variants in GCA

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

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

Position	Type	Phenotype	Significance	ClinVar
2-162356785-A-C		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCA	protein_coding	protein_coding	ENST00000437150	8	52756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000138	0.867	124910	6	832	125748	0.00334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00810	119	119	1.00	0.00000589	1424
Missense in Polyphen		23	32.281	0.71249		415
Synonymous	-1.23	48	38.3	1.25	0.00000196	387
Loss of Function	1.37	8	13.4	0.595	6.65e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00298	0.00297
Ashkenazi Jewish	0.00110	0.00109
East Asian	0.00698	0.00605
Finnish	0.0164	0.0162
European (Non-Finnish)	0.00216	0.00213
Middle Eastern	0.00698	0.00605
South Asian	0.000791	0.000719
Other	0.00296	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-binding protein that may play a role in the adhesion of neutrophils to fibronectin. May play a role in the formation of focal adhesions.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.183

Intolerance Scores

• loftool: 0.703
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.0931
• hipred: N
• hipred_score: 0.167
• ghis: 0.386

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gca
• Phenotype: immune system phenotype

Gene ontology

• Biological process: neutrophil degranulation;membrane fusion
• Cellular component: extracellular region;cytoplasm;cytosol;plasma membrane;azurophil granule lumen;extracellular exosome
• Molecular function: calcium ion binding;protein binding;protein homodimerization activity;protein heterodimerization activity