MS4A10

Summary

MS4A10 (membrane spanning 4-domains A10, HGNC:13368) is a protein-coding gene on chromosome 11q12.2, encoding Membrane-spanning 4-domains subfamily A member 10 (Q96PG2). May be involved in signal transduction as a component of a multimeric receptor complex.

Most MS4A genes, including MS4A10, encode proteins with at least 4 potential transmembrane domains and N- and C-terminal cytoplasmic domains encoded by distinct exons.

Source: NCBI Gene 341116 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_206893

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13368
Approved symbol	MS4A10
Name	membrane spanning 4-domains A10
Location	11q12.2
Locus type	gene with protein product
Status	Approved
Aliases	CD20L7, MS4A9
Ensembl gene	ENSG00000172689
Ensembl biotype	protein_coding
OMIM	608403
Entrez	341116

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000308287

RefSeq mRNA: 1 — MANE Select: NM_206893 NM_206893

CCDS: CCDS7992

Canonical transcript exons

ENST00000308287 — 8 exons

Exon	Start	End
ENSE00001168268	60790314	60790518
ENSE00001168276	60798396	60798514
ENSE00001370250	60785333	60785421
ENSE00001371173	60799828	60801305
ENSE00001379933	60790974	60791093
ENSE00001380415	60795555	60795665
ENSE00001380956	60792265	60792321
ENSE00001383000	60793972	60794103

Expression profiles

Bgee: expression breadth broad, 21 present calls, max score 96.29.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4218 / max 433.9362, expressed in 26 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114499	0.4071	26
114498	0.0121	4
114497	0.0026	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
duodenum	UBERON:0002114	96.29	gold quality
small intestine	UBERON:0002108	78.88	gold quality
small intestine Peyer’s patch	UBERON:0003454	77.91	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	51.08	silver quality
intestine	UBERON:0000160	47.28	gold quality
skeletal muscle tissue	UBERON:0001134	44.42	gold quality
adult mammalian kidney	UBERON:0000082	43.88	gold quality
kidney	UBERON:0002113	42.84	gold quality
muscle tissue	UBERON:0002385	41.55	gold quality
mucosa of transverse colon	UBERON:0004991	41.54	silver quality
bone marrow cell	CL:0002092	40.04	gold quality
transverse colon	UBERON:0001157	39.44	gold quality
lower esophagus mucosa	UBERON:0035834	37.83	gold quality
tonsil	UBERON:0002372	37.68	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
bone marrow	UBERON:0002371	37.02	gold quality
lymph node	UBERON:0000029	36.74	silver quality
monocyte	CL:0000576	36.60	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
leukocyte	CL:0000738	36.28	gold quality
colon	UBERON:0001155	35.72	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
left uterine tube	UBERON:0001303	35.18	silver quality
liver	UBERON:0002107	34.83	gold quality
granulocyte	CL:0000094	34.78	gold quality
rectum	UBERON:0001052	34.31	gold quality
smooth muscle tissue	UBERON:0001135	33.46	gold quality
placenta	UBERON:0001987	33.46	silver quality
blood	UBERON:0000178	32.62	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting MS4A10, 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-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-363-5P	99.46	64.51	1015

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	Ms4a10	ENSMUSG00000024731
rattus_norvegicus	Ms4a10	ENSRNOG00000020932

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), TMEM212 (ENSG00000186329), MS4A13 (ENSG00000204979), MS4A18 (ENSG00000214782), MS4A4E (ENSG00000214787)

Protein

Protein identifiers

Membrane-spanning 4-domains subfamily A member 10 — Q96PG2 (reviewed: Q96PG2)

Alternative names: CD20 antigen-like 7

All UniProt accessions (1): Q96PG2

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.

RefSeq proteins (1): NP_996776* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007237	CD20-like_TM	Domain
IPR030417	MS4A	Family

Pfam: PF04103

UniProt features (13 total): topological domain 5, transmembrane region 4, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PG2-F1	69.65	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 31 (showing top): MARTENS_TRETINOIN_RESPONSE_UP, BRUINS_UVC_RESPONSE_LATE, FEVR_CTNNB1_TARGETS_UP, MIR616_5P, MIR371B_5P, MIR373_5P, MIR4516, MIR6780A_5P, MIR5703, MIR4434, MIR1273H_5P, MIR6779_5P, MIR30B_3P, MIR3689A_3P_MIR3689B_3P_MIR3689C, MIR6745

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

228 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MS4A10	MS4A6E	Q96DS6	929
MS4A10	MS4A4E	Q96PG1	929
MS4A10	MS4A6A	Q9H2W1	855
MS4A10	MS4A4A	Q96JQ5	832
MS4A10	TMEM109	Q9BVC6	445
MS4A10	MS4A3	Q96HJ5	445
MS4A10	CCDC86	Q9H6F5	432
MS4A10	PPP1R37	O75864	431
MS4A10	TMEM132A	Q24JP5	406
MS4A10	PPM1N	Q8N819	400
MS4A10	MANSC1	Q9H8J5	383
MS4A10	MS4A8	Q9BY19	363
MS4A10	LUZP2	Q86TE4	350
MS4A10	AGPS	O00116	336
MS4A10	PRPF19	Q9UMS4	325
MS4A10	CDHR2	Q9BYE9	325

IntAct

3 interactions, top by confidence:

A	B	Type	Score
NEDD4	MS4A10	psi-mi:“MI:0407”(direct interaction)	0.590
MS4A10	NEDD4	psi-mi:“MI:0914”(association)	0.590

BioGRID (10): MS4A10 (Synthetic Lethality), ANKRD13A (Affinity Capture-MS), ANKRD13D (Affinity Capture-MS), DSTYK (Affinity Capture-MS), HECW2 (Affinity Capture-MS), NEDD4 (Affinity Capture-MS), APPL1 (Affinity Capture-MS), NEDD4L (Affinity Capture-MS), MS4A10 (Protein-peptide), MS4A10 (Positive Genetic)

ESM2 similar proteins: A4IIU3, A6NGA9, A6NML5, D3YWQ9, O75204, P0DP42, P11836, P13386, P19437, P20490, P56749, Q01362, Q0IIL2, Q2KHT4, Q32KQ5, Q3SZ72, Q3T110, Q3UNB8, Q3YBM2, Q497B3, Q4G068, Q504G0, Q5EB63, Q5FWC3, Q5HYL7, Q5R8D6, Q5R9K1, Q5RCD5, Q5REZ6, Q6AXT9, Q6GV27, Q7YQI4, Q8BGP5, Q8C6V3, Q8K177, Q8R1W2, Q8VHW1, Q8VI88, Q8WXS4, Q920C4

Diamond homologs: A6QPF4, P13386, P20490, Q01362, Q3C1V0, Q3C2E2, Q3UPL6, Q5REZ6, Q8N5U1, Q920C4, Q96HJ5, Q96JA4, Q96JQ5, Q96PG2, Q99N05, Q99N07, Q99N08, Q99N09, Q99N10, Q9BY19, Q9GZW8, Q9H3V2, Q9NXJ0, Q99N03, P11836, P19437, Q9H2W1, Q96DS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1163 predictions. Top by Δscore:

Variant	Effect	Δscore
11:60791056:TGCTG:T	donor_gain	1.0000
11:60793964:A:AG	acceptor_gain	1.0000
11:60793970:A:AG	acceptor_gain	1.0000
11:60793971:G:GC	acceptor_gain	1.0000
11:60793971:GA:G	acceptor_gain	1.0000
11:60793971:GAA:G	acceptor_gain	1.0000
11:60793971:GAAGA:G	acceptor_gain	1.0000
11:60794102:CGGTG:C	donor_loss	1.0000
11:60794104:G:T	donor_loss	1.0000
11:60794105:T:G	donor_loss	1.0000
11:60794106:GAG:G	donor_loss	1.0000
11:60795662:AAAGG:A	donor_loss	1.0000
11:60795663:AAGGT:A	donor_loss	1.0000
11:60795664:AGGTA:A	donor_loss	1.0000
11:60795665:GGTAA:G	donor_loss	1.0000
11:60795666:G:C	donor_loss	1.0000
11:60795667:T:G	donor_loss	1.0000
11:60791054:G:GA	donor_gain	0.9900
11:60791057:GCTGA:G	donor_gain	0.9900
11:60792522:G:GT	donor_gain	0.9900
11:60793965:C:G	acceptor_gain	0.9900
11:60793967:TATA:T	acceptor_loss	0.9900
11:60793969:TA:T	acceptor_loss	0.9900
11:60793970:A:AC	acceptor_loss	0.9900
11:60793971:G:T	acceptor_loss	0.9900
11:60794022:T:TA	acceptor_gain	0.9900
11:60794104:G:GG	donor_gain	0.9900
11:60794107:AG:A	donor_loss	0.9900
11:60795545:A:AG	acceptor_gain	0.9900
11:60795546:C:G	acceptor_gain	0.9900

AlphaMissense

1741 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:60794002:A:C	S131R	0.988
11:60794004:C:A	S131R	0.988
11:60794004:C:G	S131R	0.988
11:60791079:T:A	W97R	0.974
11:60791079:T:C	W97R	0.974
11:60794043:G:C	K144N	0.971
11:60794043:G:T	K144N	0.971
11:60794011:T:C	C134R	0.969
11:60794045:A:C	D145A	0.969
11:60791082:G:T	G98W	0.967
11:60792265:T:C	F102L	0.966
11:60792267:T:A	F102L	0.966
11:60792267:T:G	F102L	0.966
11:60794044:G:C	D145H	0.966
11:60794065:T:C	F152L	0.961
11:60794067:T:A	F152L	0.961
11:60794067:T:G	F152L	0.961
11:60795588:T:C	C176R	0.961
11:60794046:T:A	D145E	0.960
11:60794046:T:G	D145E	0.960
11:60791070:T:G	Y94D	0.958
11:60792278:G:A	G106E	0.958
11:60790993:C:A	A68D	0.957
11:60791082:G:A	G98R	0.955
11:60791082:G:C	G98R	0.955
11:60794033:T:A	V141D	0.955
11:60792277:G:A	G106R	0.954
11:60792277:G:C	G106R	0.954
11:60794024:G:A	G138D	0.954
11:60794048:T:C	L146P	0.954

dbSNP variants (sampled 300 via entrez): RS1000368961 (11:60796335 T>C), RS1000579297 (11:60797446 T>A), RS1000606901 (11:60788529 G>T), RS1000683550 (11:60799270 T>C), RS1000744751 (11:60794315 A>G,T), RS1000754265 (11:60791620 C>T), RS1000910858 (11:60785865 G>A,C), RS1001341567 (11:60786177 ACACACACACACG>A), RS1001352179 (11:60789213 C>G,T), RS1001693090 (11:60801566 T>C), RS1001721948 (11:60795392 C>T), RS1001844400 (11:60789451 G>A), RS1001893851 (11:60793400 T>C), RS1001947909 (11:60793741 C>T), RS1002190577 (11:60790981 A>C)

Disease associations

OMIM: gene MIM:608403 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Rosiglitazone	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Troglitazone	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Fenofibrate	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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