CNNM3

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

Basic information

Region (hg38): 2:96816245-96835382

Previous symbols: [ "ACDP3" ]

Links

ENSG00000168763 ∙ NCBI:26505 ∙ OMIM:607804 ∙ HGNC:104 ∙ Uniprot:Q8NE01 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNNM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNNM3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			75	2		77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	75	2	0

Variants in CNNM3

This is a list of pathogenic ClinVar variants found in the CNNM3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-96816291-T-C		not specified	Likely benign (Dec 21, 2023)
2-96816297-C-T		not specified	Uncertain significance (Dec 21, 2023)
2-96816305-C-G		not specified	Uncertain significance (Aug 12, 2021)
2-96816305-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-96816312-G-C		not specified	Uncertain significance (Oct 07, 2024)
2-96816347-G-A		not specified	Uncertain significance (Jun 26, 2024)
2-96816353-G-A		not specified	Uncertain significance (Nov 18, 2023)
2-96816363-C-T		not specified	Uncertain significance (Jan 16, 2024)
2-96816372-G-C		not specified	Uncertain significance (Oct 22, 2021)
2-96816399-A-G		not specified	Uncertain significance (Oct 06, 2024)
2-96816423-T-C		not specified	Likely benign (Dec 03, 2021)
2-96816435-C-T		not specified	Uncertain significance (Dec 03, 2024)
2-96816438-C-T		not specified	Uncertain significance (Jun 02, 2024)
2-96816491-G-T		not specified	Uncertain significance (Dec 28, 2024)
2-96816492-C-T		not specified	Uncertain significance (May 17, 2023)
2-96816530-G-A		not specified	Uncertain significance (Jan 29, 2025)
2-96816533-T-C		not specified	Uncertain significance (Jul 09, 2024)
2-96816569-C-T		not specified	Uncertain significance (Jan 24, 2025)
2-96816606-T-G		not specified	Uncertain significance (Feb 07, 2025)
2-96816618-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-96816653-G-T		not specified	Uncertain significance (Feb 22, 2023)
2-96816660-C-T		not specified	Uncertain significance (Jul 19, 2022)
2-96816675-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-96816680-T-C		not specified	Uncertain significance (Nov 09, 2023)
2-96816701-G-A		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNNM3	protein_coding	protein_coding	ENST00000305510	8	17667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.12e-7	0.893	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.756	256	292	0.876	0.0000169	4388
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000325	0.000323
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000272	0.000272
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.258
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.949

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnnm3

Gene ontology

• Biological process: ion transport
• Cellular component: plasma membrane;membrane;integral component of membrane
• Molecular function: protein binding