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): 2:96816244-96835382

Previous symbols: [ "ACDP3" ]

Links

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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (22 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	21	1	0

Variants in CNNM3

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

Position	Type	Phenotype	Significance	ClinVar
2-96816305-C-G		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
2-96816305-C-T		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
2-96816372-G-C		Inborn genetic diseases	Uncertain significance (Oct 22, 2021)
2-96816423-T-C		Inborn genetic diseases	Likely benign (Dec 03, 2021)
2-96816492-C-T		Inborn genetic diseases	Uncertain significance (May 17, 2023)
2-96816618-C-T		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
2-96816653-G-T		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
2-96816660-C-T		Inborn genetic diseases	Uncertain significance (Jul 19, 2022)
2-96816824-C-T		Inborn genetic diseases	Uncertain significance (Apr 04, 2023)
2-96816842-C-T		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
2-96816882-C-G		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
2-96816909-T-C		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
2-96816933-A-G		Inborn genetic diseases	Uncertain significance (May 06, 2022)
2-96816939-C-G		Inborn genetic diseases	Uncertain significance (Jun 27, 2023)
2-96816956-G-A		Inborn genetic diseases	Uncertain significance (Jun 23, 2023)
2-96817014-G-T		Inborn genetic diseases	Uncertain significance (Mar 11, 2022)
2-96817074-C-G		Inborn genetic diseases	Uncertain significance (May 17, 2023)
2-96817076-C-G		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
2-96817103-C-G		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
2-96817158-C-G		Inborn genetic diseases	Uncertain significance (May 09, 2022)
2-96817393-T-G		Inborn genetic diseases	Uncertain significance (Apr 17, 2023)
2-96817437-A-G		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
2-96825150-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
2-96825154-T-C		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
2-96826911-T-C		Inborn genetic diseases	Uncertain significance (Nov 10, 2021)

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