MS4A14

membrane spanning 4-domains A14, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60378529-60417756

Previous symbols: [ "MS4A16" ]

Links

ENSG00000166928 ∙ NCBI:84689 ∙ ∙ HGNC:30706 ∙ Uniprot:Q96JA4 ∙ 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 MS4A14 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A14 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	1

Variants in MS4A14

This is a list of pathogenic ClinVar variants found in the MS4A14 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)
11-60397879-A-ATT		Essential tremor	Uncertain significance (-)
11-60400407-A-G		not specified	Uncertain significance (Dec 19, 2022)
11-60400424-C-G			Benign (Jul 26, 2018)
11-60403008-T-A		not specified	Uncertain significance (Dec 06, 2022)
11-60403021-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-60415456-C-T		not specified	Uncertain significance (Feb 13, 2023)
11-60415498-A-G		not specified	Uncertain significance (Apr 07, 2022)
11-60415512-T-A		not specified	Uncertain significance (Nov 18, 2022)
11-60415543-A-T		not specified	Uncertain significance (Mar 16, 2022)
11-60415545-T-C		not specified	Uncertain significance (Sep 01, 2021)
11-60415551-A-G		not specified	Uncertain significance (Jan 16, 2024)
11-60415566-G-C		not specified	Uncertain significance (Jun 07, 2023)
11-60415590-T-C		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A14	protein_coding	protein_coding	ENST00000531783	6	39159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.71e-7	0.167	125683	0	35	125718	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0583	354	351	1.01	0.0000166	4659
Missense in Polyphen		64	61.5	1.0406		935
Synonymous	-1.56	161	138	1.17	0.00000704	1362
Loss of Function	-0.198	9	8.38	1.07	3.52e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.00	0.00
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.00	0.00
South Asian	0.000557	0.000555
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in signal transduction as a component of a multimeric receptor complex. {ECO:0000250}.

Recessive Scores

• pRec: 0.0428

Intolerance Scores

• loftool: 0.948
• rvis_EVS: 1.74
• rvis_percentile_EVS: 96.63

Haploinsufficiency Scores

• pHI: 0.0190
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a14

Gene ontology

• Cellular component: integral component of membrane