CALHM6

protein-coding

calcium homeostasis modulator family member 6, the group of Calcium homeostasis modulators

Gene summary

Predicted to enable monoatomic cation channel activity. Predicted to be involved in ATP export; monoatomic cation transmembrane transport; and regulation of natural killer cell cytokine production. Predicted to be located in immunological synapse. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf187
FAM26F

MANE transcript

NM_001010919.3

Inheritance

—

ClinVar variants

U:49B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr6:116,461,370-116,463,771

External References & Databases

Ensembl (ENSG00000188820)

Transcript & Mutation Effects

hg38 • Region Span ~2.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CALHM6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010919.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			48 clinvar	1 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	49	2	0	51

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010919.3	RefSeq	NP_001010919.1	2	MANE Select
ENST00000368605.3	Ensembl	ENSP00000357594.1	2	MANE Select
NM_001276460.2	RefSeq	NP_001263389.1	2	Standard
ENST00000368604.2	Ensembl	ENSP00000357593.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ion transport

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368605
Coding exons: 2
Length: 2402
Individuals with no LoFs: 118177
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 118178
p: 0.00000423

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.192	128	134	0.953	0.00000633	1970
Missense (PolyPhen)		34	45.675	0.74439		701
Synonymous	0.742	54	61.4	0.880	0.00000308	653
Loss of Function	0.312	3	3.64	0.824	1.57e-7	50

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000091	0.0000091	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Essentials

Essential (gene trap): N