MS4A13

Summary

MS4A13 (membrane spanning 4-domains A13, HGNC:16674) is a protein-coding gene on chromosome 11q12.2, encoding Membrane-spanning 4-domains subfamily A member 13 (Q5J8X5). May be involved in signal transduction as a component of a multimeric receptor complex.

Predicted to be involved in cell surface receptor signaling pathway. Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 503497 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_001012417

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16674
Approved symbol	MS4A13
Name	membrane spanning 4-domains A13
Location	11q12.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204979
Ensembl biotype	protein_coding
Entrez	503497

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000378185, ENST00000378186, ENST00000437058, ENST00000527948

RefSeq mRNA: 3 — MANE Select: NM_001012417 NM_001012417, NM_001100909, NM_001278320

CCDS: CCDS31571, CCDS41653, CCDS60801

Canonical transcript exons

ENST00000378186 — 7 exons

Exon	Start	End
ENSE00001476588	60542519	60542721
ENSE00001476589	60529365	60529460
ENSE00001476592	60525207	60525326
ENSE00001476594	60523897	60523953
ENSE00001476595	60518072	60518212
ENSE00001476596	60515969	60516084
ENSE00003890014	60515392	60515607

Expression profiles

Bgee: expression breadth tissue_specific, 10 present calls, max score 82.18.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0076 / max 2.9335, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114479	0.0076	4

Top tissues by expression

128 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.18	gold quality
testis	UBERON:0000473	62.57	gold quality
left testis	UBERON:0004533	62.49	gold quality
right testis	UBERON:0004534	61.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	60.27	gold quality
bone marrow cell	CL:0002092	39.22	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	33.30	gold quality
muscle tissue	UBERON:0002385	32.50	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
monocyte	CL:0000576	29.86	silver quality
leukocyte	CL:0000738	29.65	silver quality
prefrontal cortex	UBERON:0000451	29.26	gold quality
liver	UBERON:0002107	28.34	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	26.65	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
adrenal tissue	UBERON:0018303	25.76	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting MS4A13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-4689	96.97	65.79	1209
HSA-MIR-6858-5P	96.05	64.59	1020

Cross-species orthologs

26 orthologs

Organism	Symbol	Gene ID
danio_rerio	ms4a17a.6	ENSDARG00000007018
danio_rerio	ms4a17a.4	ENSDARG00000014024
danio_rerio	si:dkey-77f5.10	ENSDARG00000020548
danio_rerio	zgc:113425	ENSDARG00000026616
danio_rerio	ms4a17c.2	ENSDARG00000028659
danio_rerio	ms4a17a.7	ENSDARG00000043796
danio_rerio	ms4a17a.1	ENSDARG00000043798
danio_rerio	ms4a17a.8	ENSDARG00000043802
danio_rerio	ms4a17a.12	ENSDARG00000053563
danio_rerio	ms4a17a.16	ENSDARG00000054898
danio_rerio	si:dkey-7j14.6	ENSDARG00000090552
danio_rerio	ms4a17a.3	ENSDARG00000091970
danio_rerio	ms4a17a.5	ENSDARG00000092204
danio_rerio	si:dkey-174k12.3	ENSDARG00000092593
danio_rerio	si:dkey-238j22.1	ENSDARG00000093512
danio_rerio	si:ch73-56d11.5	ENSDARG00000093546
danio_rerio	ms4a17c.1	ENSDARG00000094643
danio_rerio	ms4a17a.11	ENSDARG00000094809
danio_rerio	ms4a17a.9	ENSDARG00000094854
danio_rerio	ms4a17a.10	ENSDARG00000095695
danio_rerio	si:ch73-56d11.3	ENSDARG00000097527
danio_rerio	tmem176l.3a	ENSDARG00000098387
danio_rerio	ms4a17a.2	ENSDARG00000105674
danio_rerio	ms4a17a.17	ENSDARG00000116378
mus_musculus	Ms4a13	ENSMUSG00000057240
rattus_norvegicus	Ms4a13	ENSRNOG00000033714

Paralogs (16): MS4A12 (ENSG00000071203), MS4A6A (ENSG00000110077), MS4A4A (ENSG00000110079), MS4A3 (ENSG00000149516), MS4A2 (ENSG00000149534), MS4A1 (ENSG00000156738), MS4A6E (ENSG00000166926), MS4A7 (ENSG00000166927), MS4A14 (ENSG00000166928), MS4A5 (ENSG00000166930), MS4A8 (ENSG00000166959), MS4A15 (ENSG00000166961), MS4A10 (ENSG00000172689), TMEM212 (ENSG00000186329), MS4A18 (ENSG00000214782), MS4A4E (ENSG00000214787)

Protein

Protein identifiers

Membrane-spanning 4-domains subfamily A member 13 — Q5J8X5 (reviewed: Q5J8X5)

Alternative names: Testis-expressed transmembrane protein 4

All UniProt accessions (2): Q5J8X5, E9PPG1

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in signal transduction as a component of a multimeric receptor complex.

Subcellular location. Membrane.

Similarity. Belongs to the MS4A family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5J8X5-1	1	yes
Q5J8X5-2	2
Q5J8X5-3	3

RefSeq proteins (3): NP_001012417, NP_001094379, NP_001265249 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007237	CD20-like_TM	Domain
IPR030417	MS4A	Family

Pfam: PF04103

UniProt features (11 total): transmembrane region 4, sequence variant 3, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5J8X5-F1	86.39	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): GTGCAAA_MIR507, MIR545_3P, MIR1185_1_3P_MIR1185_2_3P, LET_7F_2_3P, MIR507, MIR557, MIR4784, MIR3150B_3P, GSE13306_TREG_VS_TCONV_UP, GSE13306_RA_VS_UNTREATED_TCONV_UP, GSE28237_FOLLICULAR_VS_EARLY_GC_BCELL_UP, GSE28237_EARLY_VS_LATE_GC_BCELL_UP, chr11q12, GSE5589_UNSTIM_VS_45MIN_LPS_AND_IL10_STIM_MACROPHAGE_DN, GSE31622_WT_VS_KLF3_KO_BCELL_DN

GO Biological Process (1): cell surface receptor signaling pathway (GO:0007166)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
signal transduction	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

62 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MS4A13	TMEM185B	Q9H7F4	375
MS4A13	SH3TC1	Q8TE82	370
MS4A13	FAM110C	Q1W6H9	370
MS4A13	MAMDC4	Q6UXC1	348
MS4A13	PLSCR2	Q9NRY7	336
MS4A13	LRRC47	Q8N1G4	325
MS4A13	DCDC1	P59894	290
MS4A13	OPN5	Q6U736	266
MS4A13	PCDHA7	Q9UN72	263
MS4A13	FSIP2	Q5CZC0	260
MS4A13	SPAG17	Q6Q759	252
MS4A13	ODAM	A1E959	248
MS4A13	NEUROD4	Q9HD90	246
MS4A13	TACC2	O95359	227
MS4A13	CCDC40	Q4G0X9	223

IntAct

187 interactions, top by confidence:

A	B	Type	Score
MS4A13	SLC30A2	psi-mi:“MI:0915”(physical association)	0.600
MS4A13	GJA8	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	TMC4	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	LRRC3B	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	SLC7A1	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	SCN3B	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	EREG	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	RAMP1	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	GJA5	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	RNF185	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	EDA	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	CREB3L3	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	CREB3L1	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	SLC12A7	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	SPAG4	psi-mi:“MI:0915”(physical association)	0.560
KLRC1	MS4A13	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	HERPUD2	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	SLC13A4	psi-mi:“MI:0915”(physical association)	0.560
	MS4A13	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	MS4A3	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	JSRP1	psi-mi:“MI:0915”(physical association)	0.560
ASGR2	MS4A13	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	TMEM237	psi-mi:“MI:0915”(physical association)	0.560
BIK	MS4A13	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	POMK	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (63): MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid), MS4A13 (Two-hybrid)

ESM2 similar proteins: A0A2R8RY99, A4IIV4, A8MUP6, A9UL59, B2RVW2, C9JDP6, E9Q6I0, H7C241, O95859, P0DP42, P56749, Q0IIL2, Q0V9E0, Q29RH7, Q2KHT4, Q32KQ5, Q3SZT1, Q3T110, Q3UUA0, Q4V922, Q5CZV0, Q5FWC3, Q5J8X5, Q5R8B5, Q5R9K1, Q6AXT9, Q6AYL2, Q6GV27, Q6GV28, Q6ICI0, Q7T392, Q80SV1, Q80WE5, Q86WI0, Q8CJ58, Q8K445, Q8NHS1, Q8R1W2, Q8VI88, Q96CE8

Diamond homologs: Q2YDM3, Q5FWC3, Q5J8X5, Q99N10

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 60 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Gap junction assembly	6	46.2×	4e-07

GO biological processes:

GO term	Partners	Fold	FDR
cell-cell signaling	8	10.7×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

24 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1116 predictions. Top by Δscore:

Variant	Effect	Δscore
11:60515596:G:GG	donor_gain	1.0000
11:60518190:G:GT	donor_gain	1.0000
11:60515608:G:T	donor_gain	0.9900
11:60516082:GGG:G	donor_gain	0.9900
11:60516083:GGG:G	donor_gain	0.9900
11:60518690:G:GT	donor_gain	0.9900
11:60515606:GG:G	donor_gain	0.9800
11:60515607:GG:G	donor_gain	0.9800
11:60515702:AAAC:A	donor_gain	0.9800
11:60515703:AACA:A	donor_gain	0.9800
11:60515707:G:GG	donor_gain	0.9800
11:60518070:A:AG	acceptor_gain	0.9800
11:60518071:G:GG	acceptor_gain	0.9800
11:60518112:G:GA	donor_gain	0.9800
11:60518189:GGAT:G	donor_gain	0.9800
11:60518213:G:GG	donor_gain	0.9800
11:60525324:GCA:G	donor_gain	0.9800
11:60518208:TTTTT:T	donor_gain	0.9700
11:60525327:G:GG	donor_gain	0.9700
11:60515657:G:T	donor_gain	0.9600
11:60515663:G:GT	donor_gain	0.9600
11:60542517:A:AG	acceptor_gain	0.9600
11:60542518:G:GG	acceptor_gain	0.9600
11:60516083:GG:G	donor_gain	0.9500
11:60516084:GG:G	donor_gain	0.9500
11:60518178:C:G	donor_gain	0.9500
11:60516081:AGGG:A	donor_loss	0.9400
11:60516082:GGGG:G	donor_loss	0.9400
11:60516083:GGGT:G	donor_loss	0.9400
11:60516085:GT:G	donor_loss	0.9400

AlphaMissense

978 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:60518111:T:A	W10R	0.993
11:60518111:T:C	W10R	0.993
11:60518201:T:A	W40R	0.992
11:60518201:T:C	W40R	0.992
11:60518156:T:C	F25L	0.991
11:60518158:T:A	F25L	0.991
11:60518158:T:G	F25L	0.991
11:60529371:G:A	G105R	0.991
11:60529371:G:C	G105R	0.991
11:60529371:G:T	G105W	0.991
11:60518204:G:A	G41R	0.990
11:60518204:G:C	G41R	0.990
11:60529376:G:C	R106S	0.990
11:60529376:G:T	R106S	0.990
11:60525280:A:T	E87V	0.989
11:60518090:G:C	G3R	0.988
11:60525258:G:C	A80P	0.986
11:60525291:T:C	F91L	0.985
11:60525293:T:A	F91L	0.985
11:60525293:T:G	F91L	0.985
11:60518172:C:A	P30H	0.984
11:60529372:G:A	G105E	0.984
11:60525259:C:A	A80E	0.982
11:60529372:G:T	G105V	0.982
11:60525279:G:A	E87K	0.981
11:60525314:T:A	N98K	0.981
11:60525314:T:G	N98K	0.981
11:60525237:T:C	C73R	0.980
11:60525280:A:C	E87A	0.980
11:60525324:G:C	A102P	0.977

dbSNP variants (sampled 300 via entrez): RS1000027153 (11:60521365 T>C), RS1000102863 (11:60532256 G>A,T), RS1000142860 (11:60521596 A>G), RS1000172393 (11:60538871 G>C,T), RS1000492725 (11:60513891 T>C,G), RS1000525222 (11:60525418 C>A,G,T), RS1000630693 (11:60531248 G>T), RS1000718817 (11:60540749 C>T), RS1000745038 (11:60531424 A>G), RS1001032381 (11:60519665 A>G), RS1001043079 (11:60525788 C>G,T), RS1001146755 (11:60520043 A>G), RS1001225320 (11:60530925 TC>T), RS1001356028 (11:60526637 T>A,C), RS1001438489 (11:60518437 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002119_24	Metabolite levels (X-11787)	4.000000e-06
GCST004721_17	Congenital heart disease (maternal effect)	4.000000e-07
GCST005231_55	Major depressive disorder	4.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005276	hydroxy-leucine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases methylation	1
Valproic Acid	decreases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.