CALHM4

calcium homeostasis modulator family member 4, the group of Calcium homeostasis modulators

Basic information

Region (hg38): 6:116529012-116561127

Previous symbols: [ "C6orf78", "FAM26D" ]

Links

ENSG00000164451 ∙ NCBI:221301 ∙ ∙ HGNC:21094 ∙ Uniprot:Q5JW98 ∙ 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 CALHM4 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALHM4 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	3	0	0

Variants in CALHM4

This is a list of pathogenic ClinVar variants found in the CALHM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116540379-A-G		not specified	Likely benign (Dec 15, 2023)
6-116543381-A-G		not specified	Uncertain significance (Nov 17, 2022)
6-116543391-G-A		not specified	Uncertain significance (Feb 27, 2024)
6-116557838-T-C		not specified	Uncertain significance (May 28, 2023)
6-116557984-T-C		not specified	Uncertain significance (Nov 07, 2022)
6-116557987-C-T		not specified	Uncertain significance (Aug 23, 2021)
6-116558000-T-C		not specified	Uncertain significance (Oct 13, 2023)
6-116558006-G-A		not specified	Uncertain significance (Oct 27, 2023)
6-116558047-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-116558051-A-G		not specified	Uncertain significance (Mar 01, 2024)
6-116558071-T-G		not specified	Uncertain significance (Jan 30, 2024)
6-116558143-T-C		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALHM4	protein_coding	protein_coding	ENST00000405399	2	29858

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000713	0.535	125734	0	10	125744	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.480	78	90.9	0.858	0.00000438	1123
Missense in Polyphen		19	19.483	0.97522		255
Synonymous	0.179	32	33.3	0.961	0.00000165	325
Loss of Function	0.343	5	5.90	0.848	3.48e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000791	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pore-forming subunit of a voltage-gated ion channel. {ECO:0000250|UniProtKB:Q8IU99}.

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.0455
• hipred: N
• hipred_score: 0.144
• ghis: 0.465

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Calhm4

Gene ontology

• Biological process: ion transport
• Cellular component: integral component of plasma membrane