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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

ENSG00000168763NCBI:26505OMIM:607804HGNC:104Uniprot:Q8NE01AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (36 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.

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
35
clinvar
1
clinvar
36
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 35 1 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)3146557
2-96816297-C-T not specified Uncertain significance (Dec 21, 2023)3146564
2-96816305-C-G not specified Uncertain significance (Aug 12, 2021)2355215
2-96816305-C-T not specified Uncertain significance (Jul 06, 2021)2360773
2-96816353-G-A not specified Uncertain significance (Nov 18, 2023)3146575
2-96816363-C-T not specified Uncertain significance (Jan 16, 2024)3146576
2-96816372-G-C not specified Uncertain significance (Oct 22, 2021)2224453
2-96816423-T-C not specified Likely benign (Dec 03, 2021)2263302
2-96816492-C-T not specified Uncertain significance (May 17, 2023)2509802
2-96816618-C-T not specified Uncertain significance (Sep 01, 2021)2248304
2-96816653-G-T not specified Uncertain significance (Feb 22, 2023)2458331
2-96816660-C-T not specified Uncertain significance (Jul 19, 2022)2383958
2-96816675-C-T not specified Uncertain significance (Jan 30, 2024)3146567
2-96816680-T-C not specified Uncertain significance (Nov 09, 2023)3146569
2-96816701-G-A not specified Uncertain significance (Sep 22, 2023)3146570
2-96816824-C-T not specified Uncertain significance (Apr 04, 2023)2517698
2-96816839-C-G not specified Uncertain significance (Oct 04, 2022)3146571
2-96816842-C-T not specified Uncertain significance (Jul 26, 2022)2378058
2-96816858-C-A not specified Uncertain significance (Nov 09, 2023)3146572
2-96816882-C-G not specified Uncertain significance (Apr 07, 2023)2535440
2-96816909-T-C not specified Uncertain significance (Aug 30, 2021)2392513
2-96816933-A-G not specified Uncertain significance (May 06, 2022)2287910
2-96816939-C-G not specified Uncertain significance (Jun 27, 2023)2594512
2-96816956-G-A not specified Uncertain significance (Jun 23, 2023)2606223
2-96817014-G-T not specified Uncertain significance (Mar 11, 2022)2278240

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CNNM3protein_codingprotein_codingENST00000305510 817667
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.12e-70.8931257130351257480.000139
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7562562920.8760.00001694388
Missense in Polyphen96125.760.763331870
Synonymous-0.4701471401.050.000009081619
Loss of Function1.661422.50.6220.00000140258

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001810.000181
Ashkenazi Jewish0.000.00
East Asian0.0002720.000272
Finnish0.0003250.000323
European (Non-Finnish)0.0001320.000132
Middle Eastern0.0002720.000272
South Asian0.0001310.000131
Other0.000.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

pRec
0.108

Haploinsufficiency Scores

pHI
0.258
hipred
hipred_score
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cnnm3
Phenotype

Gene ontology

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