MS4A7

membrane spanning 4-domains A7, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60378485-60395951

Links

ENSG00000166927NCBI:58475OMIM:606502HGNC:13378Uniprot:Q9GZW8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MS4A7 gene.

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
clinvar
1
clinvar
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)2301300
11-60385178-T-C not specified Uncertain significance (Jan 26, 2022)2409698
11-60385191-T-C not specified Uncertain significance (Feb 10, 2022)2276479
11-60386730-G-A not specified Uncertain significance (Sep 17, 2021)2364574
11-60386732-T-G not specified Uncertain significance (Jan 24, 2024)3210808
11-60386741-A-G not specified Uncertain significance (Nov 10, 2022)2325980
11-60386747-T-A not specified Uncertain significance (Jun 19, 2024)2355164
11-60389421-G-A not specified Uncertain significance (Dec 15, 2023)3210819
11-60389423-T-G not specified Uncertain significance (May 08, 2024)3296193
11-60389424-C-T not specified Uncertain significance (May 08, 2024)3296194
11-60389487-C-A not specified Uncertain significance (Jul 30, 2023)2602085
11-60389568-A-T not specified Uncertain significance (Jan 05, 2022)2270329
11-60393790-T-C not specified Uncertain significance (Jan 11, 2023)2464153
11-60393800-C-T not specified Likely benign (Dec 12, 2023)3210830

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MS4A7protein_codingprotein_codingENST00000300184 617470
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000003480.3641257211171257390.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.02501231221.010.000005661524
Missense in Polyphen3632.6791.1016460
Synonymous0.1844950.70.9670.00000261490
Loss of Function0.384910.30.8714.31e-7139

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009060.0000904
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0001320.000123
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ms4a7
Phenotype

Gene ontology

Biological process
Cellular component
integral component of membrane
Molecular function