CNNM3

protein-coding

cyclin and CBS domain divalent metal cation transport mediator 3, the group of Cyclin and CBS domain divalent metal cation transport mediators

Gene summary

Predicted to enable transmembrane transporter activity. Predicted to be involved in magnesium ion homeostasis. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ACDP3

MANE transcript

NM_017623.5

Inheritance

—

ClinVar variants

U:141B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr2:96,816,245-96,835,382

External References & Databases

Ensembl (ENSG00000168763)

Transcript & Mutation Effects

hg38 • Region Span ~19.1 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 CNNM3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017623.5. 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			2 clinvar			2
missense			137 clinvar	3 clinvar		140
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	141	3	0	144

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017623.5	RefSeq	NP_060093.3	8	MANE Select
ENST00000305510.4	Ensembl	ENSP00000305449.3	8	MANE Select
NM_199078.3	RefSeq	NP_951060.1	7	Standard
ENST00000377060.7	Ensembl	ENSP00000366260.3	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ion transport

Molecular Function

protein binding

Cellular Component

plasma membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000305510
Coding exons: 8
Length: 17667
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125748
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.756	256	292	0.876	0.0000169	4388
Missense (PolyPhen)		96	125.76	0.76333		1870
Synonymous	-0.470	147	140	1.05	0.00000908	1619
Loss of Function	1.66	14	22.5	0.622	0.00000140	258

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable metal transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.949

Gene Damage Prediction

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