TMEM244

Summary

TMEM244 (transmembrane protein 244, HGNC:21571) is a protein-coding gene on chromosome 6q22.33, encoding Putative transmembrane protein 244 (Q5VVB8).

Predicted to be located in membrane.

Source: NCBI Gene 253582 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_001010876

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21571
Approved symbol	TMEM244
Name	transmembrane protein 244
Location	6q22.33
Locus type	gene with protein product
Status	Approved
Aliases	bA174C7.4
Ensembl gene	ENSG00000203756
Ensembl biotype	protein_coding
Entrez	253582

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000368143, ENST00000438392, ENST00000850981

RefSeq mRNA: 1 — MANE Select: NM_001010876 NM_001010876

CCDS: CCDS34536

Canonical transcript exons

ENST00000368143 — 5 exons

Exon	Start	End
ENSE00001446410	129831244	129831386
ENSE00001446411	129833460	129833585
ENSE00001446412	129843530	129843603
ENSE00001446413	129845767	129845852
ENSE00001446415	129861156	129861315

Expression profiles

Bgee: expression breadth broad, 66 present calls, max score 84.46.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4665 / max 224.4485, expressed in 113 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
75516	0.1938	60
75514	0.1295	30
75517	0.1173	47
75515	0.0259	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.46	gold quality
pituitary gland	UBERON:0000007	63.93	gold quality
adenohypophysis	UBERON:0002196	59.34	gold quality
granulocyte	CL:0000094	58.84	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	55.14	gold quality
Ammon’s horn	UBERON:0001954	53.87	gold quality
primary visual cortex	UBERON:0002436	52.46	gold quality
substantia nigra	UBERON:0002038	51.21	gold quality
amygdala	UBERON:0001876	50.88	gold quality
anterior cingulate cortex	UBERON:0009835	50.82	gold quality
temporal lobe	UBERON:0001871	50.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	50.46	gold quality
corpus callosum	UBERON:0002336	50.23	gold quality
prefrontal cortex	UBERON:0000451	49.26	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	48.59	gold quality
lymph node	UBERON:0000029	48.56	gold quality
cerebral cortex	UBERON:0000956	48.48	gold quality
frontal cortex	UBERON:0001870	45.89	gold quality
superior frontal gyrus	UBERON:0002661	45.32	gold quality
tonsil	UBERON:0002372	44.23	gold quality
bone marrow cell	CL:0002092	42.15	gold quality
brain	UBERON:0000955	41.67	gold quality
right frontal lobe	UBERON:0002810	41.13	gold quality
skeletal muscle tissue	UBERON:0001134	37.91	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow	UBERON:0002371	36.41	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
nucleus accumbens	UBERON:0001882	35.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.58

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• Hypomethylation of the promoter region drives ectopic expression of TMEM244 in Sezary cells. (PMID:32794659)
• TMEM244 Gene Expression as a Potential Blood Diagnostic Marker Distinguishing Sezary Syndrome from Mycosis Fungoides and Benign Erythroderma. (PMID:36087622)
• TMEM244 Is a Long Non-Coding RNA Necessary for CTCL Cell Growth. (PMID:36834942)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem244	ENSDARG00000043847

Paralogs (1): SYS1 (ENSG00000204070)

Protein

Protein identifiers

Putative transmembrane protein 244 — Q5VVB8 (reviewed: Q5VVB8)

All UniProt accessions (1): Q5VVB8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001010876* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019185	Integral_membrane_SYS1-rel	Family

UniProt features (8 total): sequence variant 4, transmembrane region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VVB8-F1	84.51	0.42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): chr6q22, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, TERF1_TARGET_GENES, HU_FETAL_RETINA_PHOTORECEPTOR, DESCARTES_MAIN_FETAL_PHOTORECEPTOR_CELLS, DESCARTES_FETAL_EYE_PHOTORECEPTOR_CELLS, NKX2_5_TARGET_GENES, HARALAMBIEVA_PBMC_M_M_R_II_AGE_11_22YO_VACCINATED_VS_UNVACCINATED_7YR_UP, GSE32034_UNTREATED_VS_ROSIGLIZATONE_TREATED_LY6C_LOW_MONOCYTE_DN, GSE20727_ROS_INH_VS_ROS_INH_AND_DNFB_ALLERGEN_TREATED_DC_DN

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

212 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM244	TMEM141	Q96I45	593
TMEM244	SMLR1	H3BR10	574
TMEM244	PUSL1	Q8N0Z8	559
TMEM244	C1orf115	Q9H7X2	528
TMEM244	RASGEF1C	Q8N431	526
TMEM244	LYZL4	Q96KX0	512
TMEM244	RSRC1	Q96IZ7	504
TMEM244	SNAP47	Q5SQN1	495
TMEM244	CENPBD1P	B2RD01	473
TMEM244	USF3	Q68DE3	447
TMEM244	OR2AK2	Q8NG84	447
TMEM244	CAAP1	Q9H8G2	447
TMEM244	CAPN12	Q6ZSI9	439
TMEM244	OR2L8	Q8NGY9	430
TMEM244	KIF16B	Q96L93	418

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0N0DCA4, A0A194XK05, A0A7L9EZ67, A0A8F4NUZ8, A0A8F4S726, C6Y4A4, D2I2F3, G5EEQ9, O94440, P0DXW0, P32564, P34296, P53748, Q0VD15, Q10255, Q10436, Q12155, Q29RQ9, Q3B8H0, Q53FV1, Q55E32, Q5E972, Q5R570, Q5R8X5, Q5RFN8, Q5VVB8, Q5XH57, Q5XJR6, Q5ZIU0, Q6NZZ4, Q6QI25, Q6UX40, Q74ZU2, Q86H65, Q8JFB7, Q8N138, Q8STK5, Q8SW90, Q91VP7, Q921I0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1035 predictions. Top by Δscore:

Variant	Effect	Δscore
6:129845765:A:AC	donor_gain	1.0000
6:129845766:C:CC	donor_gain	1.0000
6:129833586:C:CC	acceptor_gain	0.9900
6:129845766:CT:C	donor_gain	0.9900
6:129861155:CCTTG:C	donor_gain	0.9900
6:129833584:AACTG:A	acceptor_gain	0.9800
6:129833585:ACTG:A	acceptor_gain	0.9800
6:129833586:CTGC:C	acceptor_gain	0.9800
6:129845758:GCTAC:G	donor_loss	0.9800
6:129845759:CTACT:C	donor_loss	0.9800
6:129845760:TAC:T	donor_loss	0.9800
6:129845761:ACTTA:A	donor_loss	0.9800
6:129845762:C:CA	donor_loss	0.9800
6:129845763:T:TG	donor_loss	0.9800
6:129845764:TACTC:T	donor_loss	0.9800
6:129845765:ACTCA:A	donor_loss	0.9800
6:129845766:C:CG	donor_loss	0.9800
6:129861152:TTA:T	donor_loss	0.9800
6:129861153:TACCT:T	donor_loss	0.9800
6:129861154:ACCTT:A	donor_loss	0.9800
6:129861155:C:CA	donor_loss	0.9800
6:129833582:AGAAC:A	acceptor_gain	0.9700
6:129833583:GAACT:G	acceptor_gain	0.9700
6:129855079:AGG:A	donor_gain	0.9600
6:129861156:C:G	donor_loss	0.9600
6:129833583:GAA:G	acceptor_gain	0.9500
6:129833587:T:A	acceptor_gain	0.9500
6:129845757:TGCTA:T	donor_loss	0.9500
6:129831387:C:CC	acceptor_gain	0.9400
6:129833582:AGAA:A	acceptor_gain	0.9400

AlphaMissense

820 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:129843573:A:C	F50L	0.952
6:129843573:A:T	F50L	0.952
6:129843575:A:G	F50L	0.952
6:129843567:G:C	F52L	0.950
6:129843567:G:T	F52L	0.950
6:129843569:A:G	F52L	0.950
6:129845814:G:C	F24L	0.900
6:129845814:G:T	F24L	0.900
6:129845816:A:G	F24L	0.900
6:129831373:G:C	F111L	0.873
6:129831373:G:T	F111L	0.873
6:129831375:A:G	F111L	0.873
6:129833511:A:G	W90R	0.867
6:129833511:A:T	W90R	0.867
6:129831354:A:G	W118R	0.852
6:129831354:A:T	W118R	0.852
6:129831357:A:G	W117R	0.834
6:129831357:A:T	W117R	0.834
6:129833509:C:A	W90C	0.828
6:129833509:C:G	W90C	0.828
6:129831352:C:A	W118C	0.809
6:129831352:C:G	W118C	0.809
6:129831355:C:A	W117C	0.806
6:129831355:C:G	W117C	0.806
6:129833536:A:C	F81L	0.788
6:129833536:A:T	F81L	0.788
6:129833538:A:G	F81L	0.788
6:129831382:C:A	M108I	0.783
6:129831382:C:G	M108I	0.783
6:129831382:C:T	M108I	0.783

dbSNP variants (sampled 300 via entrez): RS1000236427 (6:129852439 T>C), RS1000358891 (6:129847173 C>A,T), RS1000368616 (6:129846897 A>T), RS1000439853 (6:129836128 C>T), RS1000475266 (6:129841301 T>C), RS1000535042 (6:129841578 A>T), RS1000571524 (6:129831928 T>A,C), RS1000588668 (6:129852767 T>A), RS1000834754 (6:129853685 A>G), RS1001005614 (6:129831651 T>A), RS1001318091 (6:129838156 C>G), RS1001342162 (6:129863034 T>G), RS1001366578 (6:129862559 A>C,G), RS1001436503 (6:129862806 T>C), RS1001509450 (6:129849599 T>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

5 associations (top):

Study	Trait	p-value
GCST001304_5	Renal sinus fat	6.000000e-06
GCST008839_463	Height	5.000000e-12
GCST008839_488	Height	5.000000e-43
GCST009597_210	Multiple sclerosis	2.000000e-07
GCST011742_49	Triglyceride levels in HIV infection	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004864	renal sinus adipose tissue measurement
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
archazolid B	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	decreases expression	1
Air Pollutants	increases expression	1
Benzo(a)pyrene	increases methylation	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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