MS4A7

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

Basic information

Region (hg38): 11:60378484-60395951

Links

ENSG00000166927 ∙ NCBI:58475 ∙ OMIM:606502 ∙ HGNC:13378 ∙ Uniprot:Q9GZW8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (9 variants)

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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	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 (Jan 26, 2022)
11-60389421-G-A		not specified	Uncertain significance (Dec 15, 2023)
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: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ms4a7

Gene ontology

• Cellular component: integral component of membrane