CALHM2

protein-coding

calcium homeostasis modulator family member 2, the group of Calcium homeostasis modulators

Gene summary

Predicted to enable monoatomic cation channel activity. Involved in ATP export and positive regulation of apoptotic process. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2025]

Previous symbols:

FAM26B

MANE transcript

NM_015916.5

Inheritance

—

ClinVar variants

U:64

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr10:103,446,786-103,452,402

External References & Databases

Ensembl (ENSG00000138172)

Transcript & Mutation Effects

hg38 • Region Span ~5.6 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 CALHM2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 62

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015916.5. 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						0
missense			64 clinvar			64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	0	0	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 101 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015916.5	RefSeq	NP_057000.2	2	MANE Select
ENST00000260743.10	Ensembl	ENSP00000260743.5	2	MANE Select
ENST00000369788.7	Ensembl	ENSP00000358803.3	2	Standard
ENST00000369788.8	Ensembl	ENSP00000358803.3	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: ENST00000260743
Coding exons: 2
Length: 6118
Individuals with no LoFs: 122725
Homozygous LoFs: 38
Heterozygous LoFs: 2984
Defined: 125747
p: 0.0121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.108	213	209	1.02	0.0000149	2085
Missense (PolyPhen)		74	76.822	0.96327		767
Synonymous	-0.409	100	94.9	1.05	0.00000692	703
Loss of Function	0.179	8	8.56	0.934	3.70e-7	101

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0023	notable
Latino/Admixed American	0.0070	0.0070	notable
Ashkenazi Jewish	0.016	0.016	notable
East Asian	0.00033	0.00033	rare
Finnish	0.035	0.035	notable
European (Non-Finnish)	0.015	0.015	notable
South Asian	0.00082	0.00082	rare
Other	0.014	0.014	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.722
RVIS EVS: 0.06
RVIS percentile EVS: 58.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.390

Gene Damage Prediction

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