HPCAL4

hippocalcin like 4, the group of EF-hand domain containing

Basic information

Region (hg38): 1:39678648-39691485

Links

ENSG00000116983 ∙ NCBI:51440 ∙ OMIM:619211 ∙ HGNC:18212 ∙ Uniprot:Q9UM19 ∙ 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 HPCAL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HPCAL4 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in HPCAL4

This is a list of pathogenic ClinVar variants found in the HPCAL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-39682545-C-T		not specified	Uncertain significance (May 09, 2023)
1-39682664-G-A		not specified	Uncertain significance (Oct 27, 2023)
1-39682670-G-T		not specified	Uncertain significance (Sep 27, 2024)
1-39682685-C-T		not specified	Uncertain significance (Feb 27, 2023)
1-39682696-C-T		not specified	Uncertain significance (Jun 13, 2022)
1-39682709-C-T		not specified	Uncertain significance (Jul 12, 2022)
1-39683989-T-G		not specified	Uncertain significance (Sep 25, 2023)
1-39683990-C-G		not specified	Uncertain significance (Feb 17, 2024)
1-39684116-G-A		not specified	Uncertain significance (Sep 14, 2021)
1-39684142-T-C		not specified	Uncertain significance (Apr 04, 2024)
1-39684447-T-C		not specified	Uncertain significance (Nov 15, 2024)
1-39684540-A-G		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HPCAL4	protein_coding	protein_coding	ENST00000372844	3	13042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000327	0.366	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.953	90	119	0.754	0.00000700	1293
Missense in Polyphen		38	53.531	0.70987		570
Synonymous	2.64	26	49.7	0.524	0.00000326	329
Loss of Function	0.164	7	7.49	0.935	3.22e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000270	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000695	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the calcium-dependent regulation of rhodopsin phosphorylation. {ECO:0000250}.

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.491
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.654
• ghis: 0.706

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.636

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hpcal4
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: signal transduction;central nervous system development
• Molecular function: calcium channel regulator activity;calcium ion binding;protein binding;protein C-terminus binding;protein domain specific binding