HPCAL1

hippocalcin like 1, the group of EF-hand domain containing

Basic information

Region (hg38): 2:10302888-10427617

Links

ENSG00000115756 ∙ NCBI:3241 ∙ OMIM:600207 ∙ HGNC:5145 ∙ Uniprot:P37235 ∙ 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 HPCAL1 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HPCAL1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in HPCAL1

This is a list of pathogenic ClinVar variants found in the HPCAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-10390199-G-T		Vascular endothelial growth factor (VEGF) inhibitor response	association (-)
2-10419893-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-10419914-G-A		not specified	Uncertain significance (Jul 13, 2022)
2-10419993-C-G		not specified	Uncertain significance (Feb 23, 2023)
2-10420134-A-G		not specified	Uncertain significance (Nov 07, 2023)
2-10423037-C-G		not specified	Uncertain significance (Mar 29, 2023)
2-10423043-A-G		not specified	Uncertain significance (Jan 17, 2024)
2-10426738-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HPCAL1	protein_coding	protein_coding	ENST00000381765	3	124729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.891	0.108	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.40	62	143	0.434	0.0000102	1303
Missense in Polyphen		18	47.877	0.37597		451
Synonymous	0.290	63	66.0	0.955	0.00000559	349
Loss of Function	2.49	0	7.19	0.00	3.05e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the calcium-dependent regulation of rhodopsin phosphorylation.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.188
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.228
• hipred: Y
• hipred_score: 0.593
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.971

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hpcal1

Gene ontology

• Cellular component: membrane
• Molecular function: calcium ion binding;protein binding