CNNM1

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

Basic information

Region (hg38): 10:99329355-99394330

Previous symbols: [ "ACDP1" ]

Links

ENSG00000119946 ∙ NCBI:26507 ∙ OMIM:607802 ∙ HGNC:102 ∙ Uniprot:Q9NRU3 ∙ 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 CNNM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNNM1 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				1	3	4
missense			44	1	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					6	6
Total	0	0	44	2	10

Variants in CNNM1

This is a list of pathogenic ClinVar variants found in the CNNM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-99329394-G-A		not specified	Uncertain significance (Oct 05, 2021)
10-99329490-C-T		not specified	Uncertain significance (Jul 20, 2021)
10-99329664-A-C		not specified	Uncertain significance (Sep 20, 2023)
10-99329671-G-A		not specified	Uncertain significance (Jan 24, 2023)
10-99329695-C-A		not specified	Uncertain significance (Feb 27, 2024)
10-99329696-T-C			Likely benign (May 01, 2022)
10-99329739-G-A		not specified	Uncertain significance (Mar 22, 2023)
10-99329746-C-A		not specified	Uncertain significance (May 08, 2023)
10-99329881-G-C		not specified	Uncertain significance (Dec 27, 2023)
10-99329913-G-C		not specified	Uncertain significance (Jan 04, 2022)
10-99330016-G-T		not specified	Uncertain significance (Aug 14, 2023)
10-99330053-G-A			Benign (May 04, 2021)
10-99330198-C-A		not specified	Uncertain significance (Feb 28, 2023)
10-99330221-G-C		not specified	Uncertain significance (Nov 07, 2023)
10-99330344-G-C		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
10-99330348-A-G		not specified	Uncertain significance (Apr 19, 2023)
10-99330357-C-T		not specified	Uncertain significance (Mar 28, 2023)
10-99330406-A-G		not specified	Uncertain significance (Apr 05, 2023)
10-99330489-G-A			Likely benign (Mar 29, 2018)
10-99330565-C-T		not specified	Uncertain significance (Sep 14, 2022)
10-99330671-T-G			Benign (May 04, 2021)
10-99330936-A-G		not specified	Uncertain significance (Jan 26, 2022)
10-99357551-A-C		not specified	Uncertain significance (Sep 29, 2023)
10-99357800-G-A			Benign (May 10, 2021)
10-99360867-C-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNNM1	protein_coding	protein_coding	ENST00000356713	11	65232

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0176	0.982	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	334	508	0.657	0.0000296	5976
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000651	0.000624
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000112	0.000105
Middle Eastern	0.000219	0.000217
South Asian	0.000106	0.0000980
Other	0.000355	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0984

Haploinsufficiency Scores

• pHI: 0.176
• hipred: Y
• hipred_score: 0.809
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.460

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnnm1

Gene ontology

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