TMEM60

Summary

TMEM60 (transmembrane protein 60, HGNC:21754) is a protein-coding gene on chromosome 7q11.23, encoding Transmembrane protein 60 (Q9H2L4).

Predicted to be located in membrane.

Source: NCBI Gene 85025 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 23 total
• MANE Select transcript: NM_032936

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21754
Approved symbol	TMEM60
Name	transmembrane protein 60
Location	7q11.23
Locus type	gene with protein product
Status	Approved
Aliases	DC32
Ensembl gene	ENSG00000135211
Ensembl biotype	protein_coding
Entrez	85025

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000257663, ENST00000858200, ENST00000926858, ENST00000926859, ENST00000926860, ENST00000968240

RefSeq mRNA: 1 — MANE Select: NM_032936 NM_032936

CCDS: CCDS5593

Canonical transcript exons

ENST00000257663 — 2 exons

Exon	Start	End
ENSE00001090748	77798254	77798434
ENSE00001428380	77793728	77794423

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 99.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.1578 / max 283.0321, expressed in 1803 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
84473	23.1578	1803

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.50	gold quality
oocyte	CL:0000023	98.54	gold quality
ileal mucosa	UBERON:0000331	95.53	gold quality
islet of Langerhans	UBERON:0000006	95.38	gold quality
tibialis anterior	UBERON:0001385	93.87	gold quality
monocyte	CL:0000576	92.90	gold quality
leukocyte	CL:0000738	92.89	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.61	gold quality
epithelial cell of pancreas	CL:0000083	92.60	gold quality
pancreatic ductal cell	CL:0002079	92.11	gold quality
germinal epithelium of ovary	UBERON:0001304	91.98	gold quality
upper arm skin	UBERON:0004263	91.23	silver quality
pigmented layer of retina	UBERON:0001782	91.11	gold quality
retina	UBERON:0000966	91.09	gold quality
esophagus squamous epithelium	UBERON:0006920	91.03	gold quality
rectum	UBERON:0001052	90.55	gold quality
deltoid	UBERON:0001476	90.55	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.43	gold quality
calcaneal tendon	UBERON:0003701	90.28	gold quality
mucosa of transverse colon	UBERON:0004991	90.25	gold quality
kidney epithelium	UBERON:0004819	90.24	silver quality
granulocyte	CL:0000094	90.05	gold quality
adult organism	UBERON:0007023	90.05	gold quality
pancreas	UBERON:0001264	89.97	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.74	gold quality
smooth muscle tissue	UBERON:0001135	89.54	gold quality
sperm	CL:0000019	89.48	silver quality
lymph node	UBERON:0000029	89.37	gold quality
metanephros	UBERON:0000081	89.27	gold quality
parietal pleura	UBERON:0002400	89.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting TMEM60, 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-3688-3P	99.97	72.02	2834
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-105-5P	99.54	69.24	2060
HSA-MIR-7853-5P	99.54	69.30	2055
HSA-MIR-4728-3P	99.47	68.94	981
HSA-MIR-653-5P	99.46	67.35	1300
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-4635	98.74	67.63	1339
HSA-MIR-6764-3P	98.44	67.64	1153
HSA-MIR-6824-3P	98.44	67.62	1154
HSA-MIR-4277	98.34	67.17	1323
HSA-MIR-376C-3P	97.63	68.88	1263
HSA-MIR-4695-3P	96.71	67.21	836
HSA-MIR-3976	96.67	67.79	1187
HSA-MIR-563	96.26	66.13	450
HSA-MIR-4774-5P	95.92	68.27	827
HSA-MIR-380-5P	95.68	67.32	512

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tmem60	ENSMUSG00000045435
rattus_norvegicus	Tmem60	ENSRNOG00000013510
drosophila_melanogaster	CG13919	FBGN0035248

Paralogs (2): TMEM185B (ENSG00000226479), TMEM185A (ENSG00000269556)

Protein

Protein identifiers

Transmembrane protein 60 — Q9H2L4 (reviewed: Q9H2L4)

All UniProt accessions (1): Q9H2L4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_116325* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019396	TM_Fragile-X-F-assoc	Family

Pfam: PF10269

UniProt features (6 total): transmembrane region 4, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H2L4-F1	77.43	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 88 (showing top): RNGTGGGC_UNKNOWN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN, chr7q11, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, STAT5A_01, MYB_Q6, TCANNTGAY_SREBP1_01, DELACROIX_RAR_BOUND_ES, FORTSCHEGGER_PHF8_TARGETS_DN, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, GREB1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM60	TVP23B	Q9NYZ1	687
TMEM60	FAM229B	Q4G0N7	569
TMEM60	WDR37	Q9Y2I8	559
TMEM60	TMEM120A	Q9BXJ8	506
TMEM60	WDR72	Q3MJ13	504
TMEM60	TMEM120B	A0PK00	495
TMEM60	ANXA9	O76027	480
TMEM60	SLC6A13	Q9NSD5	448
TMEM60	PHTF2	Q8N3S3	433
TMEM60	NPIPB9	F8W1W9	420
TMEM60	ANKRD65	E5RJM6	419
TMEM60	TFDP2	Q14188	412
TMEM60	TMEM236	Q5W0B7	405
TMEM60	SLC22A2	O15244	404
TMEM60	ZNF570	Q96NI8	380

IntAct

296 interactions, top by confidence:

A	B	Type	Score
TMEM60	GPR61	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	HSD17B11	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	ERVFRD-1	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	SLC6A15	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	LEPROTL1	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	IL10RA	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	SLC39A1	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	IL7R	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	SAR1A	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	ANKS6	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	LRRC3B	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	CPLX4	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	SPNS3	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	LHFPL5	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	PAGE1	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	GJA8	psi-mi:“MI:0915”(physical association)	0.560
TMEM60	SCN3B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (91): TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid), TMEM60 (Two-hybrid)

ESM2 similar proteins: A0A078H868, B3Y064, B9RK42, B9TRX0, O14038, O15243, O65085, O76767, O89013, P38312, P48583, P49858, P52159, P53173, Q09473, Q0DET3, Q0IHJ0, Q0VGV9, Q22361, Q28FY5, Q2QQ55, Q3EDD7, Q3SYT0, Q3ZBX1, Q561T9, Q5F433, Q5PR61, Q5PSV5, Q5XH84, Q5ZJD9, Q658I5, Q66I08, Q6DGL7, Q6GNX5, Q6PFS5, Q7SYR6, Q84W04, Q8GWT5, Q8K174, Q8R1L4

Diamond homologs: Q8K174, Q9H2L4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 95 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
R-HSA-425366	5	18.1×	4e-04
SLC-mediated transmembrane transport	8	9.5×	1e-04
Transport of small molecules	13	6.5×	8e-06

GO biological processes:

GO term	Partners	Fold	FDR
transmembrane transport	5	9.8×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

472 predictions. Top by Δscore:

Variant	Effect	Δscore
7:77798970:CGGTA:C	donor_loss	0.9900
7:77798971:GGTAA:G	donor_loss	0.9900
7:77798972:G:GG	donor_gain	0.9900
7:77798972:G:T	donor_loss	0.9900
7:77798973:T:G	donor_loss	0.9900
7:77794404:C:CT	acceptor_gain	0.9800
7:77794422:CC:C	acceptor_gain	0.9800
7:77794423:CC:C	acceptor_gain	0.9800
7:77797455:A:C	donor_gain	0.9800
7:77798249:CTCA:C	donor_loss	0.9800
7:77798250:TCA:T	donor_loss	0.9800
7:77798251:CAC:C	donor_loss	0.9800
7:77798252:ACCT:A	donor_loss	0.9800
7:77799042:G:GT	donor_gain	0.9700
7:77799233:TCCTC:T	donor_gain	0.9700
7:77794405:G:T	acceptor_gain	0.9600
7:77797454:A:AC	donor_gain	0.9500
7:77798388:T:TA	donor_gain	0.9500
7:77798399:T:TA	donor_gain	0.9500
7:77799058:G:GT	donor_gain	0.9500
7:77799059:G:T	donor_gain	0.9500
7:77794424:CT:C	acceptor_loss	0.9400
7:77794425:T:G	acceptor_loss	0.9400
7:77798248:ACTC:A	donor_loss	0.9400
7:77798252:A:AC	donor_gain	0.9400
7:77798253:C:CC	donor_gain	0.9400
7:77794420:TACC:T	acceptor_gain	0.9300
7:77794426:A:C	acceptor_loss	0.9200
7:77799002:GGGC:G	donor_gain	0.9100
7:77798253:CCTGG:C	donor_gain	0.9000

AlphaMissense

862 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:77794247:A:G	W43R	0.996
7:77794247:A:T	W43R	0.996
7:77794337:A:G	W13R	0.995
7:77794337:A:T	W13R	0.995
7:77794252:G:T	P41Q	0.993
7:77794252:G:C	P41R	0.992
7:77794034:A:G	W114R	0.991
7:77794034:A:T	W114R	0.991
7:77794271:A:G	W35R	0.991
7:77794271:A:T	W35R	0.991
7:77794039:G:C	P112R	0.990
7:77794039:G:T	P112H	0.988
7:77794104:G:C	F90L	0.988
7:77794104:G:T	F90L	0.988
7:77794106:A:G	F90L	0.988
7:77794237:T:A	D46V	0.987
7:77794261:A:T	I38K	0.986
7:77794019:C:G	G119R	0.985
7:77794019:C:T	G119R	0.985
7:77794237:T:G	D46A	0.985
7:77794243:A:T	I44K	0.985
7:77794090:C:T	C95Y	0.983
7:77794089:A:C	C95W	0.982
7:77794238:C:G	D46H	0.981
7:77794091:A:G	C95R	0.980
7:77794018:C:T	G119E	0.979
7:77794093:A:T	L94H	0.979
7:77794294:A:G	L27P	0.977
7:77794253:G:A	P41S	0.976
7:77794296:T:A	K26N	0.976

dbSNP variants (sampled 300 via entrez): RS1000437122 (7:77797066 C>A), RS1001528735 (7:77793445 T>C), RS1002109094 (7:77798689 C>T), RS1002131340 (7:77795473 C>T), RS1002526919 (7:77795093 G>A), RS1002589054 (7:77795708 T>G), RS1002661115 (7:77795406 T>C), RS1003012796 (7:77796899 A>G), RS1004267015 (7:77793334 A>C,T), RS1004445909 (7:77799509 C>G,T), RS1004739143 (7:77793550 C>T), RS1005401260 (7:77796748 C>G), RS1005495726 (7:77794681 G>C), RS1005555974 (7:77800024 G>A), RS1006405913 (7:77795337 T>A,C)

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

9 associations (top):

Study	Trait	p-value
GCST000649_15	Chronic kidney disease	2.000000e-09
GCST003372_19	Glomerular filtration rate (creatinine)	8.000000e-13
GCST003401_18	Glomerular filtration rate in non diabetics (creatinine)	1.000000e-12
GCST004292_46	Glomerular filtration rate (creatinine)	1.000000e-09
GCST007344_73	Estimated glomerular filtration rate	1.000000e-15
GCST008058_169	Estimated glomerular filtration rate	2.000000e-36
GCST008061_3	Estimated glomerular filtration rate	3.000000e-06
GCST008745_65	Estimated glomerular filtration rate in non-diabetics	6.000000e-15
GCST008747_28	Estimated glomerular filtration rate	2.000000e-23

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance	3
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1
MT19c compound	increases expression	1
Temozolomide	decreases expression	1
Acetaminophen	increases expression	1
Cadmium	decreases expression	1
Coal	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Quercetin	decreases expression	1
Silver	decreases expression	1
Smoke	decreases expression, increases abundance	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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