TMEM42

Summary

TMEM42 (transmembrane protein 42, HGNC:28444) is a protein-coding gene on chromosome 3p21.31, encoding Transmembrane protein 42 (Q69YG0).

Predicted to be located in membrane.

Source: NCBI Gene 131616 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• MANE Select transcript: NM_144638

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28444
Approved symbol	TMEM42
Name	transmembrane protein 42
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	MGC29956
Ensembl gene	ENSG00000169964
Ensembl biotype	protein_coding
Entrez	131616

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000302392, ENST00000477126, ENST00000891867, ENST00000891868, ENST00000891869

RefSeq mRNA: 1 — MANE Select: NM_144638 NM_144638

CCDS: CCDS2722

Canonical transcript exons

ENST00000302392 — 3 exons

Exon	Start	End
ENSE00001156953	44861912	44862116
ENSE00001166960	44864197	44864343
ENSE00003623072	44865040	44865664

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 92.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.0086 / max 91.3018, expressed in 1744 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36350	18.0086	1744

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	92.24	gold quality
hypothalamus	UBERON:0001898	92.21	gold quality
substantia nigra	UBERON:0002038	92.06	gold quality
nucleus accumbens	UBERON:0001882	91.47	gold quality
Ammon’s horn	UBERON:0001954	91.41	gold quality
amygdala	UBERON:0001876	91.32	gold quality
temporal lobe	UBERON:0001871	91.30	gold quality
putamen	UBERON:0001874	91.29	gold quality
pituitary gland	UBERON:0000007	91.13	gold quality
caudate nucleus	UBERON:0001873	90.64	gold quality
adenohypophysis	UBERON:0002196	90.64	gold quality
left testis	UBERON:0004533	90.19	gold quality
right testis	UBERON:0004534	90.09	gold quality
right adrenal gland	UBERON:0001233	89.91	gold quality
anterior cingulate cortex	UBERON:0009835	89.54	gold quality
testis	UBERON:0000473	89.42	gold quality
right uterine tube	UBERON:0001302	89.34	gold quality
right adrenal gland cortex	UBERON:0035827	89.28	gold quality
cerebral cortex	UBERON:0000956	88.99	gold quality
prefrontal cortex	UBERON:0000451	88.97	gold quality
brain	UBERON:0000955	88.93	gold quality
right lobe of thyroid gland	UBERON:0001119	88.92	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.87	gold quality
left adrenal gland	UBERON:0001234	88.74	gold quality
right frontal lobe	UBERON:0002810	88.62	gold quality
frontal cortex	UBERON:0001870	88.60	gold quality
Brodmann (1909) area 9	UBERON:0013540	88.60	gold quality
left lobe of thyroid gland	UBERON:0001120	88.59	gold quality
left adrenal gland cortex	UBERON:0035825	88.55	gold quality
apex of heart	UBERON:0002098	88.35	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting TMEM42, 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-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-196A-3P	99.19	67.34	1204
HSA-MIR-6797-3P	99.17	66.94	668
HSA-MIR-877-3P	99.09	68.10	1637
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-5590-5P	98.81	68.78	969
HSA-MIR-5000-3P	98.79	65.63	1251
HSA-MIR-6076	98.61	65.69	637
HSA-MIR-4436A	98.05	64.83	1140
HSA-MIR-6881-3P	98.04	68.24	1777
HSA-MIR-892B	98.00	67.11	821
HSA-MIR-4700-3P	97.74	68.64	1014

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem42a	ENSDARG00000102717
danio_rerio	tmem42b	ENSDARG00000103817
mus_musculus	Tmem42	ENSMUSG00000066233
drosophila_melanogaster	CG42495	FBGN0260027
caenorhabditis_elegans		WBGENE00009576

Protein

Protein identifiers

Transmembrane protein 42 — Q69YG0 (reviewed: Q69YG0)

All UniProt accessions (1): Q69YG0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_653239* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037185	EmrE-like	Homologous_superfamily
IPR039632	TMEM42	Family

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q69YG0-F1	72.31	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, HAMAI_APOPTOSIS_VIA_TRAIL_DN, ESC_V6.5_UP_EARLY.V1_UP, RB_DN.V1_DN, chr3p21, GSE14415_ACT_VS_CTRL_NATURAL_TREG_DN, CBX7_TARGET_GENES, NFE2L1_TARGET_GENES, PITX1_TARGET_GENES, ZNF423_TARGET_GENES, ZSCAN31_TARGET_GENES, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP, MIR5590_5P, MIR4700_3P

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

410 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM42	C5orf52	A6NGY3	541
TMEM42	CFAP97D1	B2RV13	512
TMEM42	IQCE	Q6IPM2	400
TMEM42	CCDC24	Q8N4L8	393
TMEM42	ZDHHC3	Q9NYG2	392
TMEM42	ZBTB9	Q96C00	391
TMEM42	WFDC5	Q8TCV5	390
TMEM42	TLCD5	Q6ZRR5	380
TMEM42	SPMIP9	Q96LM6	376
TMEM42	TMEM125	Q96AQ2	373
TMEM42	CCDC116	Q8IYX3	372
TMEM42	FHIP1A	Q05DH4	368
TMEM42	TMEM156	Q8N614	358
TMEM42	SLC35G2	Q8TBE7	352
TMEM42	DNAJC5G	Q8N7S2	350

IntAct

158 interactions, top by confidence:

A	B	Type	Score
TMEM42	REEP2	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	AQP3	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	MRM1	psi-mi:“MI:0915”(physical association)	0.560
TMEM42		psi-mi:“MI:0915”(physical association)	0.560
TMEM42	SVOPL	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	NEMP1	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	TM4SF19	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	LHFPL5	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	ZDHHC15	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	MTIF3	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	HSD17B13	psi-mi:“MI:0915”(physical association)	0.560
RABAC1	TMEM42	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	RETREG3	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	GJA8	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	EDA	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	MFF	psi-mi:“MI:0915”(physical association)	0.560
	TMEM42	psi-mi:“MI:0915”(physical association)	0.560
TMEM42	RBPMS	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (59): TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid), TMEM42 (Two-hybrid)

ESM2 similar proteins: A6NFX1, A6QQL0, D2HKB0, D3ZG27, F1NCD6, F1NJ67, O09014, O70496, O82390, P51798, P51799, Q17QZ3, Q1JQC1, Q32LQ6, Q3T9M1, Q3T9X0, Q3TIT8, Q4PKH3, Q504N2, Q58CV5, Q5F3N0, Q5R8G5, Q5RB09, Q5T4D3, Q5ZIT9, Q5ZKS8, Q66H95, Q68F72, Q69YG0, Q6AY78, Q6PDE8, Q7SY29, Q8BFQ6, Q8BG19, Q8GX78, Q8IVW8, Q8IZD6, Q8N697, Q8NCC5, Q8NEB5

Diamond homologs: Q2KIX3, Q5R7Q1, Q69YG0, Q9CR22

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

567 predictions. Top by Δscore:

Variant	Effect	Δscore
3:44862039:G:GT	donor_gain	0.9900
3:44862039:G:T	donor_gain	0.9700
3:44862182:G:GT	donor_gain	0.9700
3:44862128:G:GT	donor_gain	0.9600
3:44862352:GT:G	donor_gain	0.9600
3:44862114:G:GT	donor_gain	0.9500
3:44862128:G:T	donor_gain	0.9400
3:44861921:C:T	donor_gain	0.9300
3:44865038:A:AG	acceptor_gain	0.9300
3:44865039:G:GG	acceptor_gain	0.9300
3:44862360:G:GA	donor_gain	0.9200
3:44862013:C:T	donor_gain	0.9100
3:44862147:C:G	donor_gain	0.9100
3:44862011:GGCGG:G	donor_gain	0.9000
3:44862012:GCGGG:G	donor_gain	0.9000
3:44862136:T:A	donor_gain	0.9000
3:44861991:G:GT	donor_gain	0.8900
3:44862359:T:TA	donor_gain	0.8900
3:44862400:GGACC:G	donor_gain	0.8900
3:44864339:GCTCG:G	donor_gain	0.8900
3:44865034:TCGCA:T	acceptor_loss	0.8900
3:44865035:CGCA:C	acceptor_loss	0.8900
3:44865036:GCA:G	acceptor_loss	0.8900
3:44865037:CA:C	acceptor_loss	0.8900
3:44865038:AGGC:A	acceptor_loss	0.8900
3:44865039:G:GA	acceptor_loss	0.8900
3:44862134:G:GG	donor_gain	0.8800
3:44862186:G:T	donor_gain	0.8800
3:44865030:T:A	acceptor_loss	0.8800
3:44862401:G:T	donor_gain	0.8700

AlphaMissense

1022 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:44864257:T:A	W85R	0.998
3:44864257:T:C	W85R	0.998
3:44862064:G:A	G47D	0.997
3:44862063:G:C	G47R	0.996
3:44862072:G:A	G50R	0.996
3:44862072:G:C	G50R	0.996
3:44862073:G:A	G50E	0.996
3:44864275:G:C	G91R	0.996
3:44864331:T:A	N109K	0.996
3:44864331:T:G	N109K	0.996
3:44862051:T:C	C43R	0.995
3:44862053:T:G	C43W	0.995
3:44862061:C:A	A46D	0.995
3:44864247:T:A	N81K	0.995
3:44864247:T:G	N81K	0.995
3:44864256:G:A	M84I	0.995
3:44864256:G:C	M84I	0.995
3:44864256:G:T	M84I	0.995
3:44864279:T:C	L92P	0.995
3:44865088:T:A	W130R	0.995
3:44865088:T:C	W130R	0.995
3:44865116:G:A	G139E	0.995
3:44862063:G:T	G47C	0.994
3:44862072:G:T	G50W	0.994
3:44862082:C:A	A53D	0.994
3:44864276:G:A	G91D	0.994
3:44865085:T:A	W129R	0.994
3:44865085:T:C	W129R	0.994
3:44865115:G:A	G139R	0.994
3:44865115:G:C	G139R	0.994

dbSNP variants (sampled 300 via entrez): RS1000817454 (3:44865062 A>G,T), RS1000861034 (3:44861605 G>A), RS1000909091 (3:44864673 G>C), RS1001819457 (3:44863647 G>A), RS1001914306 (3:44863351 A>G), RS1002819311 (3:44862464 C>A), RS1002872444 (3:44864049 G>A,T), RS1002915752 (3:44861926 T>A,C), RS1003701364 (3:44860008 G>A), RS1003801345 (3:44861345 C>G,T), RS1003937155 (3:44861191 A>G), RS1004749761 (3:44865867 G>A), RS1005714240 (3:44864039 G>A,T), RS1006229888 (3:44865255 T>C), RS1007058442 (3:44864506 G>A)

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

2 associations (top):

Study	Trait	p-value
GCST002481_7	Acne (severe)	3.000000e-06
GCST008103_52	Bipolar disorder	3.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	4
bisphenol A	increases expression, affects cotreatment	2
sodium arsenite	affects methylation, decreases expression	2
Estradiol	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Decitabine	affects expression	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects expression	1
Copper	affects binding, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Disulfiram	affects binding, increases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, increases expression	1
Lead	affects expression	1
Methyl Methanesulfonate	increases expression	1
Niclosamide	increases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Tretinoin	increases expression	1
Tunicamycin	increases expression	1

Clinical trials (associated diseases)

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