MS4A3

membrane spanning 4-domains A3, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60056587-60071115

Previous symbols: [ "CD20L" ]

Links

ENSG00000149516 ∙ NCBI:932 ∙ OMIM:606498 ∙ HGNC:7317 ∙ Uniprot:Q96HJ5 ∙ 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 MS4A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A3 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in MS4A3

This is a list of pathogenic ClinVar variants found in the MS4A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60061190-G-T		not specified	Uncertain significance (Jan 27, 2022)
11-60061221-G-C		not specified	Uncertain significance (May 22, 2023)
11-60061308-G-C		not specified	Uncertain significance (May 06, 2022)
11-60062489-G-A		not specified	Uncertain significance (Apr 26, 2023)
11-60062489-G-C		not specified	Uncertain significance (Apr 25, 2022)
11-60062493-T-A		not specified	Uncertain significance (May 23, 2023)
11-60062534-C-G		not specified	Uncertain significance (Apr 20, 2024)
11-60062541-A-G		not specified	Uncertain significance (Oct 17, 2023)
11-60062568-C-T		not specified	Likely benign (Feb 22, 2023)
11-60064262-T-C		not specified	Uncertain significance (Jun 18, 2024)
11-60064278-C-A		not specified	Uncertain significance (Apr 17, 2023)
11-60067039-T-G		not specified	Uncertain significance (Mar 20, 2023)
11-60067040-C-G		not specified	Uncertain significance (Mar 28, 2023)
11-60067086-T-A		not specified	Uncertain significance (Apr 26, 2024)
11-60069581-T-C		not specified	Uncertain significance (Jul 13, 2022)
11-60069619-G-A		not specified	Likely benign (Dec 13, 2021)
11-60069635-T-C		not specified	Uncertain significance (Jan 23, 2024)
11-60069650-A-G		not specified	Uncertain significance (May 03, 2023)
11-60069673-G-A		not specified	Uncertain significance (Apr 29, 2024)
11-60070226-C-T		not specified	Uncertain significance (Sep 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A3	protein_coding	protein_coding	ENST00000278865	6	14542

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000263	0.543	125727	0	9	125736	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.487	122	108	1.13	0.00000498	1371
Missense in Polyphen		26	28.936	0.89854		371
Synonymous	0.615	38	43.1	0.881	0.00000225	436
Loss of Function	0.655	8	10.3	0.780	4.35e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hematopoietic modulator for the G1-S cell cycle transition. Modulates the level of phosphorylation of cyclin- dependent kinase 2 (CDK2) through its direct binding to cyclin- dependent kinase inhibitor 3 (CDKN3/KAP). {ECO:0000269|PubMed:11781350}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0506

Intolerance Scores

• loftool: 0.850
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.0731
• hipred: N
• hipred_score: 0.123
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000765

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a3

Gene ontology

• Biological process: neutrophil degranulation;regulation of cell cycle
• Cellular component: plasma membrane;integral component of membrane;specific granule membrane;perinuclear region of cytoplasm
• Molecular function: protein binding