CNNM1

protein-coding

cyclin and CBS domain divalent metal cation transport mediator 1, the group of Cyclin and CBS domain divalent metal cation transport mediators

Gene summary

This gene encodes a member of the ancient conserved domain protein family. The encoded protein may bind copper. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

Previous symbols:

ACDP1

MANE transcript

NM_020348.3

Inheritance

—

ClinVar variants

U:118B:3

Top phenotype

Breast ductal adenocarcinoma

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr10:99,329,356-99,394,330

External References & Databases

Ensembl (ENSG00000119946)

Transcript & Mutation Effects

hg38 • Region Span ~65.0 kb

Loading mutation effect viewer...

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 CNNM1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 110

not providedTotal: 4

Breast ductal adenocarcinomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020348.3. 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 clinvar	2
missense			115 clinvar	1 clinvar		116
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	118	2	1	121

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020348.3	RefSeq	NP_065081.2	11	MANE Select
ENST00000356713.5	Ensembl	ENSP00000349147.4	11	MANE Select
NM_001345887.2	RefSeq	NP_001332816.1	12	Standard
NM_001345888.2	RefSeq	NP_001332817.1	10	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
integral component of membrane
dendrite
neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356713
Coding exons: 11
Length: 65232
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 125748
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.74	334	508	0.657	0.0000296	5976
Missense (PolyPhen)		97	206.94	0.46873		2324
Synonymous	1.57	194	224	0.866	0.0000131	2053
Loss of Function	3.61	9	30.5	0.295	0.00000148	385

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00015	0.00012	rare
Latino/Admixed American	0.00050	0.00049	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00011	0.000098	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0984

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.460

Gene Damage Prediction

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