TMEM238

Summary

TMEM238 (transmembrane protein 238, HGNC:40042) is a protein-coding gene on chromosome 19q13.42, encoding Transmembrane protein 238 (C9JI98).

Predicted to be located in membrane.

Source: NCBI Gene 388564 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 21 total
• MANE Select transcript: NM_001190764

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40042
Approved symbol	TMEM238
Name	transmembrane protein 238
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000233493
Ensembl biotype	protein_coding
Entrez	388564

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000444469, ENST00000967957

RefSeq mRNA: 1 — MANE Select: NM_001190764 NM_001190764

CCDS: CCDS54323

Canonical transcript exons

ENST00000444469 — 2 exons

Exon	Start	End
ENSE00001708649	55383722	55384292
ENSE00002233649	55379244	55379367

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 92.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.1995 / max 376.9822, expressed in 1553 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182798	26.1995	1553

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	92.52	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.59	gold quality
lower esophagus mucosa	UBERON:0035834	83.38	gold quality
body of pancreas	UBERON:0001150	81.71	gold quality
duodenum	UBERON:0002114	81.65	gold quality
right lobe of liver	UBERON:0001114	80.44	gold quality
esophagus mucosa	UBERON:0002469	79.94	gold quality
transverse colon	UBERON:0001157	79.22	gold quality
minor salivary gland	UBERON:0001830	79.14	gold quality
saliva-secreting gland	UBERON:0001044	78.57	gold quality
liver	UBERON:0002107	77.95	gold quality
skin of abdomen	UBERON:0001416	77.49	gold quality
adult mammalian kidney	UBERON:0000082	77.07	gold quality
left lobe of thyroid gland	UBERON:0001120	76.98	gold quality
right lobe of thyroid gland	UBERON:0001119	76.79	gold quality
zone of skin	UBERON:0000014	76.52	gold quality
skin of leg	UBERON:0001511	76.51	gold quality
right uterine tube	UBERON:0001302	75.83	gold quality
small intestine Peyer’s patch	UBERON:0003454	75.06	gold quality
body of stomach	UBERON:0001161	75.03	gold quality
thyroid gland	UBERON:0002046	75.01	gold quality
small intestine	UBERON:0002108	74.65	gold quality
metanephros cortex	UBERON:0010533	73.91	gold quality
granulocyte	CL:0000094	73.15	gold quality
stomach	UBERON:0000945	72.32	gold quality
pancreas	UBERON:0001264	71.95	gold quality
prostate gland	UBERON:0002367	71.92	gold quality
blood	UBERON:0000178	71.45	gold quality
upper lobe of left lung	UBERON:0008952	70.89	gold quality
bone marrow cell	CL:0002092	70.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting TMEM238, 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-7152-3P	99.97	67.47	849
HSA-MIR-505-5P	97.01	65.54	778
HSA-MIR-4264	96.35	64.76	1480

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem238a	ENSDARG00000093684
mus_musculus	Tmem238	ENSMUSG00000030431
rattus_norvegicus	Tmem238	ENSRNOG00000070914

Protein

Protein identifiers

Transmembrane protein 238 — C9JI98 (reviewed: C9JI98)

All UniProt accessions (1): C9JI98

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001177693* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029365	TMEM238	Family

Pfam: PF15125

UniProt features (12 total): topological domain 3, transmembrane region 2, region of interest 2, compositionally biased region 2, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JI98-F1	68.30	0.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 175

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): CUI_TCF21_TARGETS_2_UP, MEISSNER_NPC_HCP_WITH_H3K4ME2, LI_INDUCED_T_TO_NATURAL_KILLER_UP, BRUINS_UVC_RESPONSE_LATE, EBNA1BP2_TARGET_GENES, MIR4264, POU2AF1_TARGET_GENES, MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN, MEBARKI_HCC_PROGENITOR_FZD8CRD_DN, DESCARTES_FETAL_HEART_ERYTHROBLASTS, ZNF579_TARGET_GENES, QI_PBMC_ZOSTAVAX_AGE_50_75YO_CORRELATED_WITH_EXPANSION_OF_VZV_SPECIFIC_T_CELLS_TO_PEAK_AT_1DY_NEGATIVE, QI_PBMC_ZOSTAVAX_AGE_50_75YO_CORRELATED_WITH_CONTRACTION_OF_VZV_SPECIFIC_T_CELLS_PEAK_TO_28DYAT_1DY_NEGATIVE, HOEK_NK_CELL_2011_2012_TIV_1D_VS_0DY_ADULT_1D_DN, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

214 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM238	SULT6B1	Q6IMI4	570
TMEM238	TMEM53	Q6P2H8	549
TMEM238	TMEM223	A0PJW6	525
TMEM238	RFXAP	O00287	515
TMEM238	TMEM147	Q9BVK8	452
TMEM238	TMEM151A	Q8N4L1	434
TMEM238	TMEM154	Q6P9G4	413
TMEM238	TMEM38A	Q9H6F2	371
TMEM238	DNAAF1	Q8NEP3	345
TMEM238	LYPD2	Q6UXB3	318
TMEM238	IGSF10	Q6WRI0	314
TMEM238	SLC26A5	P58743	309
TMEM238	TMEM238L	A6NJY4	295
TMEM238	ATP6V1G1	O75348	273
TMEM238	RPL28	P46779	245

IntAct

2 interactions, top by confidence:

A	B	Type	Score
TRDN	TMEM223	psi-mi:“MI:0914”(association)	0.640

BioGRID (1): TMEM238 (Affinity Capture-RNA)

ESM2 similar proteins: A0A8I5KY20, A2A9T0, A2IDD5, B0BNK9, B8ZZ34, C9JI98, C9JLR9, F5GYI3, O18734, P0CG25, P84157, Q0IIA6, Q0PHV7, Q0X0E2, Q13387, Q1RMK9, Q2M3D2, Q2TAM9, Q3ZCQ3, Q4VA45, Q673H1, Q69YZ2, Q6NS60, Q6P6N5, Q6PJ61, Q7Z6J2, Q80ZJ8, Q810I0, Q86SX3, Q86UD0, Q86XT2, Q8BNN1, Q8IUW3, Q8N4Y2, Q8N6N2, Q8QZV0, Q8R4T5, Q8TF61, Q8VCR9, Q8WXF8

Diamond homologs: A6NJY4, A9JSM3, C9JI98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

233 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55383717:CTCA:C	donor_loss	0.9700
19:55383718:TCAC:T	donor_loss	0.9700
19:55383719:CACCT:C	donor_loss	0.9700
19:55383720:A:AG	donor_loss	0.9700
19:55383721:C:CG	donor_loss	0.9700
19:55383732:CTCG:C	donor_gain	0.9700
19:55383731:A:AC	donor_gain	0.9600
19:55383732:C:CC	donor_gain	0.9600
19:55379368:C:CC	acceptor_gain	0.9200
19:55383961:T:TA	donor_gain	0.8400
19:55379365:TGT:T	acceptor_gain	0.7700
19:55379365:TGTC:T	acceptor_loss	0.7500
19:55379367:TCT:T	acceptor_loss	0.7500
19:55379368:C:CG	acceptor_loss	0.7500
19:55379369:T:G	acceptor_loss	0.7500
19:55383606:TC:T	donor_gain	0.7400
19:55383909:G:A	donor_gain	0.7400
19:55379370:G:C	acceptor_loss	0.7200
19:55383716:CCTCA:C	donor_gain	0.6900
19:55383717:CTCAC:C	donor_gain	0.6900
19:55383727:C:CA	donor_gain	0.6900
19:55383889:G:T	donor_gain	0.6900
19:55381418:C:G	acceptor_gain	0.6800
19:55383607:C:CT	donor_gain	0.6800
19:55383608:T:TT	donor_gain	0.6800
19:55379364:TTGT:T	acceptor_gain	0.6700
19:55379366:GT:G	acceptor_gain	0.6700
19:55383720:A:AC	donor_gain	0.6600
19:55383721:C:CC	donor_gain	0.6600
19:55383733:T:C	donor_gain	0.6600

AlphaMissense

1071 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:55383995:A:G	W89R	1.000
19:55383995:A:T	W89R	1.000
19:55384004:A:G	W86R	1.000
19:55384004:A:T	W86R	1.000
19:55383981:G:C	N93K	0.999
19:55383981:G:T	N93K	0.999
19:55384002:C:A	W86C	0.999
19:55384002:C:G	W86C	0.999
19:55384007:C:G	G85R	0.999
19:55384014:G:C	S82R	0.999
19:55384014:G:T	S82R	0.999
19:55384015:C:A	S82I	0.999
19:55384016:T:G	S82R	0.999
19:55384036:C:T	G75D	0.999
19:55384037:C:G	G75R	0.999
19:55384096:C:T	G55D	0.999
19:55384097:C:G	G55R	0.999
19:55384117:C:T	G48D	0.999
19:55384118:C:G	G48R	0.999
19:55383973:A:G	I96T	0.998
19:55383979:A:T	I94N	0.998
19:55383982:T:A	N93I	0.998
19:55383993:C:A	W89C	0.998
19:55383993:C:G	W89C	0.998
19:55384006:C:T	G85D	0.998
19:55384015:C:T	S82N	0.998
19:55384020:G:C	F80L	0.998
19:55384020:G:T	F80L	0.998
19:55384022:A:G	F80L	0.998
19:55384037:C:A	G75C	0.998

dbSNP variants (sampled 300 via entrez): RS1000302654 (19:55386249 T>G), RS1000426297 (19:55380677 G>A), RS1000594492 (19:55385528 A>C), RS1000744197 (19:55379195 C>G), RS1000775961 (19:55380511 G>A,C), RS1001161805 (19:55379425 G>A), RS1001597950 (19:55381058 G>A), RS1001694788 (19:55383463 G>A,T), RS1001819350 (19:55385929 T>C), RS1002330228 (19:55379605 G>A,C), RS1002377490 (19:55383747 C>T), RS1002432800 (19:55385860 T>A,C), RS1002598912 (19:55382402 G>A), RS1002692347 (19:55382684 G>A), RS1003757303 (19:55379381 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
tri-o-cresyl phosphate	decreases expression	1
ICG 001	increases expression	1
bisphenol B	decreases expression	1
bisphenol Z	decreases 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	affects expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Glucose	decreases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Aflatoxin B1	decreases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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