CNNM1
Basic information
Region (hg38): 10:99329356-99394330
Previous symbols: [ "ACDP1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 4 | |||||
missense | 44 | 46 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 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) | ||
10-99329424-G-A | not specified | Uncertain significance (May 06, 2024) | ||
10-99329434-G-A | not specified | Uncertain significance (May 14, 2024) | ||
10-99329490-C-T | not specified | Uncertain significance (Jul 20, 2021) | ||
10-99329561-G-C | not specified | Uncertain significance (Mar 18, 2024) | ||
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) | ||
10-99330033-G-A | not specified | Uncertain significance (May 14, 2024) | ||
10-99330053-G-A | Benign (May 04, 2021) | |||
10-99330073-C-A | not specified | Uncertain significance (May 15, 2024) | ||
10-99330156-C-G | not specified | Uncertain significance (Apr 26, 2024) | ||
10-99330198-C-A | not specified | Uncertain significance (Feb 28, 2023) | ||
10-99330221-G-C | not specified | Uncertain significance (Nov 07, 2023) | ||
10-99330283-G-T | not specified | Uncertain significance (Apr 06, 2024) | ||
10-99330319-G-C | not specified | Uncertain significance (Jun 07, 2024) | ||
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) |
GnomAD
Source:
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:
- 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
- Phenotype
Gene ontology
- Biological process
- ion transport
- Cellular component
- plasma membrane;integral component of membrane;dendrite;neuronal cell body
- Molecular function
- protein binding