MS4A7
Basic information
Region (hg38): 11:60378485-60395951
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 MS4A7 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 | 11 | 12 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 11 | 1 | 0 |
Variants in MS4A7
This is a list of pathogenic ClinVar variants found in the MS4A7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-60385105-T-G | not specified | Uncertain significance (Jul 13, 2022) | ||
11-60385178-T-C | not specified | Uncertain significance (Jan 26, 2022) | ||
11-60385191-T-C | not specified | Uncertain significance (Feb 10, 2022) | ||
11-60386730-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
11-60386732-T-G | not specified | Uncertain significance (Jan 24, 2024) | ||
11-60386741-A-G | not specified | Uncertain significance (Nov 10, 2022) | ||
11-60386747-T-A | not specified | Uncertain significance (Jun 19, 2024) | ||
11-60389421-G-A | not specified | Uncertain significance (Dec 15, 2023) | ||
11-60389423-T-G | not specified | Uncertain significance (May 08, 2024) | ||
11-60389424-C-T | not specified | Uncertain significance (May 08, 2024) | ||
11-60389487-C-A | not specified | Uncertain significance (Jul 30, 2023) | ||
11-60389568-A-T | not specified | Uncertain significance (Jan 05, 2022) | ||
11-60393790-T-C | not specified | Uncertain significance (Jan 11, 2023) | ||
11-60393800-C-T | not specified | Likely benign (Dec 12, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MS4A7 | protein_coding | protein_coding | ENST00000300184 | 6 | 17470 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000348 | 0.364 | 125721 | 1 | 17 | 125739 | 0.0000716 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0250 | 123 | 122 | 1.01 | 0.00000566 | 1524 |
Missense in Polyphen | 36 | 32.679 | 1.1016 | 460 | ||
Synonymous | 0.184 | 49 | 50.7 | 0.967 | 0.00000261 | 490 |
Loss of Function | 0.384 | 9 | 10.3 | 0.871 | 4.31e-7 | 139 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000906 | 0.0000904 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000132 | 0.000123 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in signal transduction as a component of a multimeric receptor complex.;
Intolerance Scores
- loftool
- 0.973
- rvis_EVS
- 1.04
- rvis_percentile_EVS
- 91.21
Haploinsufficiency Scores
- pHI
- 0.0604
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.404
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.715
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ms4a7
- Phenotype
Gene ontology
- Biological process
- Cellular component
- integral component of membrane
- Molecular function