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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

ENSG00000119946NCBI:26507OMIM:607802HGNC:102Uniprot:Q9NRU3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNNM1 gene.

  • Inborn genetic diseases (30 variants)
  • not provided (12 variants)

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
clinvar
3
clinvar
4
missense
30
clinvar
1
clinvar
1
clinvar
32
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
6
clinvar
6
Total 0 0 30 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 Inborn genetic diseases Uncertain significance (Oct 05, 2021)2253286
10-99329490-C-T Inborn genetic diseases Uncertain significance (Jul 20, 2021)2306913
10-99329671-G-A Inborn genetic diseases Uncertain significance (Jan 24, 2023)2478426
10-99329696-T-C Likely benign (May 01, 2022)2640745
10-99329739-G-A Inborn genetic diseases Uncertain significance (Mar 22, 2023)2525513
10-99329746-C-A Inborn genetic diseases Uncertain significance (May 08, 2023)2545002
10-99329913-G-C Inborn genetic diseases Uncertain significance (Jan 04, 2022)2222554
10-99330016-G-T Inborn genetic diseases Uncertain significance (Aug 14, 2023)2591612
10-99330053-G-A Benign (May 04, 2021)1181501
10-99330198-C-A Inborn genetic diseases Uncertain significance (Feb 28, 2023)2490180
10-99330344-G-C Breast ductal adenocarcinoma Uncertain significance (Jul 20, 2015)221303
10-99330348-A-G Inborn genetic diseases Uncertain significance (Apr 19, 2023)2539037
10-99330357-C-T Inborn genetic diseases Uncertain significance (Mar 28, 2023)2530762
10-99330406-A-G Inborn genetic diseases Uncertain significance (Apr 05, 2023)2533612
10-99330489-G-A Likely benign (Mar 29, 2018)713121
10-99330565-C-T Inborn genetic diseases Uncertain significance (Sep 14, 2022)2360009
10-99330671-T-G Benign (May 04, 2021)1297924
10-99330936-A-G Inborn genetic diseases Uncertain significance (Jan 26, 2022)2350430
10-99357800-G-A Benign (May 10, 2021)1270983
10-99360913-C-T Inborn genetic diseases Uncertain significance (Mar 07, 2023)2495166
10-99360925-T-G Inborn genetic diseases Uncertain significance (Jan 06, 2023)2474219
10-99361030-C-T Benign (May 10, 2021)1268829
10-99362239-T-C Inborn genetic diseases Uncertain significance (Jan 26, 2023)2479804
10-99362295-G-A Inborn genetic diseases Uncertain significance (May 17, 2023)2547730
10-99362307-C-G Inborn genetic diseases Uncertain significance (May 23, 2023)2509439

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CNNM1protein_codingprotein_codingENST00000356713 1165232
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01760.9821257050431257480.000171
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.743345080.6570.00002965976
Missense in Polyphen97206.940.468732324
Synonymous1.571942240.8660.00001312053
Loss of Function3.61930.50.2950.00000148385

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006510.000624
Ashkenazi Jewish0.000.00
East Asian0.0002190.000217
Finnish0.0001410.000139
European (Non-Finnish)0.0001120.000105
Middle Eastern0.0002190.000217
South Asian0.0001060.0000980
Other0.0003550.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cnnm1
Phenotype

Gene ontology

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