TMEM250

Summary

TMEM250 (transmembrane protein 250, HGNC:31009) is a protein-coding gene on chromosome 9q34.3, encoding Transmembrane protein 250 (H0YL14). May play a role in cell proliferation by promoting progression into S phase.

Involved in positive regulation of cell population proliferation and positive regulation of viral process. Located in cytoplasm and nucleoplasm.

Source: NCBI Gene 90120 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_152833

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31009
Approved symbol	TMEM250
Name	transmembrane protein 250
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	bA83N9.1
Ensembl gene	ENSG00000238227
Ensembl biotype	protein_coding
Entrez	90120

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 nonsense_mediated_decay

ENST00000418388, ENST00000447934, ENST00000448040, ENST00000557985, ENST00000561457, ENST00000873032, ENST00000873033, ENST00000873034, ENST00000912634, ENST00000912635, ENST00000912636, ENST00000912637

RefSeq mRNA: 2 — MANE Select: NM_152833 NM_001256526, NM_152833

CCDS: CCDS59155

Canonical transcript exons

ENST00000418388 — 2 exons

Exon	Start	End
ENSE00001606746	136118485	136118875
ENSE00003844590	136114589	136117024

Expression profiles

Bgee: expression breadth ubiquitous, 223 present calls, max score 91.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.5147 / max 90.7847, expressed in 1796 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103125	11.8414	1767
103124	3.3404	1593
103123	2.9001	1540
103121	1.4331	826
103122	1.0857	818
103120	0.9141	512

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	91.48	gold quality
mucosa of transverse colon	UBERON:0004991	91.02	gold quality
ileal mucosa	UBERON:0000331	89.55	gold quality
apex of heart	UBERON:0002098	89.17	gold quality
lower esophagus mucosa	UBERON:0035834	88.96	gold quality
right frontal lobe	UBERON:0002810	88.35	gold quality
gastrocnemius	UBERON:0001388	88.24	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.11	gold quality
leukocyte	CL:0000738	88.01	gold quality
monocyte	CL:0000576	87.78	gold quality
muscle of leg	UBERON:0001383	87.74	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.43	gold quality
esophagus mucosa	UBERON:0002469	87.32	gold quality
anterior cingulate cortex	UBERON:0009835	87.21	gold quality
putamen	UBERON:0001874	86.85	gold quality
stromal cell of endometrium	CL:0002255	86.77	gold quality
transverse colon	UBERON:0001157	86.63	gold quality
esophagus	UBERON:0001043	86.55	gold quality
gingival epithelium	UBERON:0001949	86.54	silver quality
prefrontal cortex	UBERON:0000451	86.45	gold quality
lower esophagus	UBERON:0013473	86.34	gold quality
nucleus accumbens	UBERON:0001882	86.32	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.32	gold quality
caudate nucleus	UBERON:0001873	86.29	gold quality
right coronary artery	UBERON:0001625	86.24	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	86.08	gold quality
muscle layer of sigmoid colon	UBERON:0035805	86.07	gold quality
blood	UBERON:0000178	85.89	gold quality
frontal cortex	UBERON:0001870	85.80	gold quality
neocortex	UBERON:0001950	85.71	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting TMEM250, 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-4283	100.00	66.42	2097
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6764-5P	99.75	67.89	2304

Literature-anchored findings (GeneRIF, showing 1)

• This study examined host cell protein C9orf69, which promotes viral proliferation via interaction with HSV-1 UL25 protein. (PMID:21667337)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tmem250	ENSMUSG00000087679
rattus_norvegicus	Tmem250	ENSRNOG00000042501
drosophila_melanogaster	Septin2	FBGN0014029
caenorhabditis_elegans		WBGENE00006795

Paralogs (12): SEPTIN3 (ENSG00000100167), SEPTIN7 (ENSG00000122545), SEPTIN6 (ENSG00000125354), SEPTIN11 (ENSG00000138758), SEPTIN12 (ENSG00000140623), SEPTIN14 (ENSG00000154997), SEPTIN8 (ENSG00000164402), SEPTIN2 (ENSG00000168385), SEPTIN1 (ENSG00000180096), SEPTIN9 (ENSG00000184640), SEPTIN5 (ENSG00000184702), SEPTIN10 (ENSG00000186522)

Protein

Protein identifiers

Transmembrane protein 250 — H0YL14 (reviewed: H0YL14)

Alternative names: Herpes virus UL25-binding protein

All UniProt accessions (3): H0YL14, H3BQM9, H3BVA3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cell proliferation by promoting progression into S phase. (Microbial infection) Promotes human herpes simplex virus 1/HHV-1 proliferation.

Subunit / interactions. (Microbial infection) Interacts with herpes simplex virus 1/HHV-1 protein CVC2/UL25.

Subcellular location. Membrane. Nucleus. Cytoplasm.

Induction. Up-regulated upon HHV-1 infection.

RefSeq proteins (2): NP_001243455, NP_690046* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR041156	TM250	Family

Pfam: PF17685

UniProt features (3 total): transmembrane region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H0YL14-F1	75.08	0.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): MODULE_255, MODULE_317, GOBP_POSITIVE_REGULATION_OF_VIRAL_PROCESS, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, MODULE_69, GOBP_POSITIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION, MODULE_37, GCNP_SHH_UP_EARLY.V1_UP, MTOR_UP.N4.V1_DN, chr9q34, DROSHA_TARGET_GENES, FOXE1_TARGET_GENES, HMG20B_TARGET_GENES, HOXB6_TARGET_GENES, ID2_TARGET_GENES

GO Biological Process (2): positive regulation of cell population proliferation (GO:0008284), positive regulation of viral process (GO:0048524)

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

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
viral process	1
positive regulation of biological process	1
regulation of viral process	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

138 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM250	CT47A11	Q5JQC4	505
TMEM250	SLC35E2B	P0CK96	505
TMEM250	WBP2NL	Q6ICG8	480
TMEM250	EXD3	Q8N9H8	426
TMEM250	G2E3	Q7L622	418
TMEM250	CCDC9B	Q6ZUT6	368
TMEM250	ADSS2	P30520	365
TMEM250	DOCK9	Q9BZ29	359
TMEM250	NPHP1	O15259	327
TMEM250	ATAD1	Q8NBU5	322
TMEM250	TMEM51	Q9NW97	248
TMEM250	PLCB1	Q9NQ66	233
TMEM250	DCP1B	Q8IZD4	220
TMEM250	SUGP1	Q8IWZ8	204
TMEM250	ATF3	P18847	181

IntAct

9 interactions, top by confidence:

A	B	Type	Score
UL25	TMEM250	psi-mi:“MI:0915”(physical association)	0.460
TMEM250	UL25	psi-mi:“MI:0403”(colocalization)	0.460
TMEM250	CVC2	psi-mi:“MI:0915”(physical association)	0.370
SLC39A14	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC6A12	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC7A1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): C9orf69 (Affinity Capture-RNA), C9orf69 (Affinity Capture-MS), C9orf69 (Affinity Capture-MS), C9orf69 (Affinity Capture-MS)

ESM2 similar proteins: A0A3B3IS91, A0A455ZAR2, A0A6I8MX38, A0A6I8PU40, C0HLZ6, D3DTV9, H0YL14, I3L0S3, L7N648, O70738, O83165, O90299, P03289, P07116, P09697, P09698, P0DI83, P12064, P14505, P16814, P25133, P29164, P55693, P69616, P69617, P89476, Q04221, Q04612, Q2J4A0, Q5JLA7, Q5R4B0, Q64364, Q6GZW8, Q6IPW1, Q6ZSA8, Q81870, Q8N1I8, Q8N726, Q8N7S6, Q8N9T2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

412 predictions. Top by Δscore:

Variant	Effect	Δscore
9:136118082:C:CA	donor_gain	0.9900
9:136118132:AAGG:A	donor_gain	0.9900
9:136118253:C:A	donor_gain	0.9900
9:136118306:T:TA	donor_gain	0.9900
9:136117797:CAGA:C	donor_gain	0.9800
9:136118156:G:A	donor_gain	0.9800
9:136118192:A:AC	donor_gain	0.9800
9:136118415:T:TA	donor_gain	0.9800
9:136118186:C:CT	donor_gain	0.9700
9:136118191:CAA:C	donor_gain	0.9700
9:136118192:AAA:A	donor_gain	0.9700
9:136118192:AAACG:A	donor_gain	0.9700
9:136118193:A:C	donor_gain	0.9700
9:136117346:T:A	donor_gain	0.9600
9:136118139:G:A	donor_gain	0.9500
9:136118187:C:CT	donor_gain	0.9500
9:136117025:CT:C	acceptor_loss	0.9400
9:136118195:CGCGA:C	donor_gain	0.9400
9:136118246:T:TA	donor_gain	0.9400
9:136118345:C:CA	donor_gain	0.9400
9:136117025:C:CC	acceptor_gain	0.9300
9:136117028:C:CT	acceptor_gain	0.9300
9:136117114:TCCAG:T	donor_gain	0.9300
9:136117115:CCAGC:C	donor_gain	0.9300
9:136118198:G:GT	donor_gain	0.9300
9:136118209:G:C	donor_gain	0.9300
9:136117796:A:AC	donor_gain	0.9200
9:136117797:C:CC	donor_gain	0.9200
9:136118124:C:A	donor_gain	0.9200
9:136118290:TGG:T	donor_gain	0.9200

AlphaMissense

881 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:136116712:G:C	S63R	0.993
9:136116712:G:T	S63R	0.993
9:136116714:T:G	S63R	0.993
9:136116718:G:C	S61R	0.989
9:136116718:G:T	S61R	0.989
9:136116720:T:G	S61R	0.989
9:136116862:G:C	F13L	0.987
9:136116862:G:T	F13L	0.987
9:136116864:A:G	F13L	0.987
9:136116493:G:C	F136L	0.982
9:136116493:G:T	F136L	0.982
9:136116495:A:G	F136L	0.982
9:136116519:C:G	G128R	0.963
9:136116733:G:C	F56L	0.963
9:136116733:G:T	F56L	0.963
9:136116735:A:G	F56L	0.963
9:136116507:A:G	C132R	0.961
9:136116510:A:G	W131R	0.960
9:136116510:A:T	W131R	0.960
9:136116717:A:G	C62R	0.960
9:136116513:C:G	G130R	0.958
9:136116518:C:T	G128D	0.949
9:136116502:G:C	F133L	0.948
9:136116502:G:T	F133L	0.948
9:136116504:A:G	F133L	0.948
9:136116512:C:T	G130D	0.947
9:136116884:A:G	I6T	0.946
9:136116693:A:G	W70R	0.943
9:136116693:A:T	W70R	0.943
9:136116522:C:G	G127R	0.942

dbSNP variants (sampled 300 via entrez): RS1000105977 (9:136120063 A>G), RS1000203128 (9:136117981 T>A), RS1000256877 (9:136118135 G>A), RS1000464037 (9:136117858 G>A,C), RS1000741686 (9:136108361 C>G), RS1000897080 (9:136114835 A>G), RS1001155210 (9:136112234 A>T), RS1001576960 (9:136112258 G>T), RS1001660865 (9:136118196 G>C), RS1001714588 (9:136118420 G>A,C), RS1001986755 (9:136112499 G>A,T), RS1002076889 (9:136108833 G>A,C,T), RS1002108290 (9:136108983 A>G), RS1002231340 (9:136118597 C>T), RS1002603583 (9:136109952 G>A,T)

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

5 associations (top):

Study	Trait	p-value
GCST004131_21	Inflammatory bowel disease	5.000000e-36
GCST004132_11	Crohn’s disease	6.000000e-30
GCST004133_17	Ulcerative colitis	2.000000e-16
GCST005023_18	Initial pursuit acceleration	6.000000e-06
GCST011741_38	LDL cholesterol levels in HIV infection	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008434	initial pursuit acceleration
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Cadmium Chloride	decreases expression, increases expression	2
aminomethylphosphonic acid (AMPA)	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
benzo(e)pyrene	decreases methylation	1
ferrous chloride	decreases expression	1
cupric chloride	increases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Bleomycin	increases expression	1
Camptothecin	increases expression	1
Cisplatin	increases expression	1
Deoxyglucose	increases expression	1
Doxorubicin	increases expression	1
Gallic Acid	decreases expression	1
Hydroxyurea	increases expression	1
Methapyrilene	decreases methylation	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Valproic Acid	increases methylation	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Aflatoxin B1	increases methylation	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1LV	Abcam HeLa C9orf69 KO	Cancer cell line	Female
CVCL_D9UG	Ubigene HEK293 TMEM250 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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