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.

• not_specified (18 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000139249.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			14	4		18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	5	0

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