MS4A6E

membrane spanning 4-domains A6E, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60327255-60396596

Links

ENSG00000166926 ∙ NCBI:245802 ∙ OMIM:608402 ∙ HGNC:14285 ∙ Uniprot:Q96DS6 ∙ 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 MS4A6E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A6E 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				1		1
missense			10	3		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	4	0

Variants in MS4A6E

This is a list of pathogenic ClinVar variants found in the MS4A6E region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-60334902-T-A		not specified	Uncertain significance (Dec 07, 2021)
11-60334908-C-T		not specified	Uncertain significance (Mar 27, 2023)
11-60334918-A-G		not specified	Uncertain significance (Dec 12, 2023)
11-60334919-T-G		not specified	Uncertain significance (Nov 08, 2022)
11-60334935-C-T		not specified	Uncertain significance (May 06, 2022)
11-60334954-A-G		not specified	Uncertain significance (Dec 02, 2022)
11-60334977-G-A		not specified	Likely benign (Mar 31, 2024)
11-60335013-C-T		not specified	Uncertain significance (Apr 13, 2022)
11-60337817-C-T		not specified	Likely benign (Aug 02, 2022)
11-60337907-C-T		not specified	Likely benign (Jan 23, 2023)
11-60337918-G-C		not specified	Uncertain significance (Nov 06, 2023)
11-60337928-G-A		not specified	Uncertain significance (Sep 07, 2022)
11-60339904-G-A			Likely benign (Apr 01, 2021)
11-60339905-T-A		not specified	Uncertain significance (Oct 17, 2023)
11-60339936-A-G		not specified	Likely benign (Aug 13, 2021)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A6E	protein_coding	protein_coding	ENST00000300182	3	61766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0292	0.817	125699	0	24	125723	0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.504	89	76.6	1.16	0.00000371	937
Missense in Polyphen		14	21.192	0.66062		303
Synonymous	-0.674	36	31.2	1.15	0.00000163	308
Loss of Function	1.10	3	5.87	0.511	2.48e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00190	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00190	0.00109
South Asian	0.0000653	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.

Recessive Scores

• pRec: 0.0389

Intolerance Scores

• loftool: 0.667
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.00560
• hipred: N
• hipred_score: 0.132

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a6d

Gene ontology

• Cellular component: integral component of membrane