CALHM3

protein-coding

calcium homeostasis modulator 3, the group of Calcium homeostasis modulators

Gene summary

Predicted to enable monoatomic cation channel activity and voltage-gated monoatomic ion channel activity. Predicted to be involved in ATP transport; protein heterooligomerization; and sensory perception of taste. Predicted to be located in basolateral plasma membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM26A

MANE transcript

NM_001129742.2

Inheritance

—

ClinVar variants

U:65B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr10:103,472,804-103,479,240

External References & Databases

Ensembl (ENSG00000183128)

Transcript & Mutation Effects

hg38 • Region Span ~6.4 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 CALHM3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 68

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001129742.2. 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			65 clinvar	4 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	4	0	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001129742.2	RefSeq	NP_001123214.1	3	MANE Select
ENST00000369783.4	Ensembl	ENSP00000358798.4	3	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ion transport

Molecular Function

protein binding

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369783
Coding exons: 3
Length: 6437
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.347	186	200	0.931	0.0000138	2182
Missense (PolyPhen)		75	69.377	1.081		760
Synonymous	0.983	83	95.2	0.872	0.00000652	753
Loss of Function	1.18	5	8.79	0.569	3.76e-7	101

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	0.0	absent
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}.;

Recessive Scores

pRec: 0.0963

Intolerance Scores

RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.355

Gene Damage Prediction

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