TMEM44

Summary

TMEM44 (transmembrane protein 44, HGNC:25120) is a protein-coding gene on chromosome 3q29, encoding Transmembrane protein 44 (Q2T9K0).

Predicted to enable basic amino acid transmembrane transporter activity. Predicted to be involved in basic amino acid transmembrane transport. Predicted to be located in membrane.

Source: NCBI Gene 93109 — RefSeq curated summary.

At a glance

• GWAS associations: 68
• Clinical variants (ClinVar): 115 total
• MANE Select transcript: NM_001011655

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25120
Approved symbol	TMEM44
Name	transmembrane protein 44
Location	3q29
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp686O18124
Ensembl gene	ENSG00000145014
Ensembl biotype	protein_coding
Entrez	93109

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 18 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000330115, ENST00000347147, ENST00000381975, ENST00000392432, ENST00000419280, ENST00000429560, ENST00000430601, ENST00000432352, ENST00000452358, ENST00000467284, ENST00000473092, ENST00000476750, ENST00000477651, ENST00000494894, ENST00000870306, ENST00000936586, ENST00000936587, ENST00000936588, ENST00000936589, ENST00000943212, ENST00000943213, ENST00000943214, ENST00000943215, ENST00000943216

RefSeq mRNA: 4 — MANE Select: NM_001011655 NM_001011655, NM_001166305, NM_001166306, NM_138399

CCDS: CCDS3308, CCDS33921, CCDS54698, CCDS54699

Canonical transcript exons

ENST00000347147 — 10 exons

Exon	Start	End
ENSE00001691426	194587678	194588639
ENSE00003499411	194615569	194615697
ENSE00003509401	194625897	194625990
ENSE00003519753	194628383	194628509
ENSE00003606880	194604287	194604445
ENSE00003613217	194617099	194617269
ENSE00003614463	194610916	194611020
ENSE00003636851	194623529	194623695
ENSE00003661116	194623224	194623310
ENSE00003909130	194633079	194633419

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 93.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.0984 / max 119.1715, expressed in 1618 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46248	5.0739	1518
46249	1.5508	1040
46250	0.4737	245

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	93.37	gold quality
right lung	UBERON:0002167	93.12	gold quality
cortical plate	UBERON:0005343	92.15	gold quality
transverse colon	UBERON:0001157	89.01	gold quality
apex of heart	UBERON:0002098	88.94	gold quality
upper lobe of left lung	UBERON:0008952	88.47	gold quality
lower esophagus mucosa	UBERON:0035834	87.35	gold quality
rectum	UBERON:0001052	87.13	gold quality
stromal cell of endometrium	CL:0002255	87.08	gold quality
upper lobe of lung	UBERON:0008948	87.01	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.25	gold quality
omental fat pad	UBERON:0010414	85.74	gold quality
sural nerve	UBERON:0015488	85.73	gold quality
peritoneum	UBERON:0002358	85.68	gold quality
spleen	UBERON:0002106	85.58	gold quality
minor salivary gland	UBERON:0001830	85.35	gold quality
caudate nucleus	UBERON:0001873	85.35	gold quality
putamen	UBERON:0001874	85.23	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.93	gold quality
tibial nerve	UBERON:0001323	84.87	gold quality
endocervix	UBERON:0000458	84.66	gold quality
adipose tissue of abdominal region	UBERON:0007808	84.60	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.32	gold quality
subcutaneous adipose tissue	UBERON:0002190	84.30	gold quality
ectocervix	UBERON:0012249	83.98	gold quality
ganglionic eminence	UBERON:0004023	83.66	gold quality
anterior cingulate cortex	UBERON:0009835	83.54	gold quality
right frontal lobe	UBERON:0002810	83.46	gold quality
metanephros cortex	UBERON:0010533	83.13	gold quality
left uterine tube	UBERON:0001303	83.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.75

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting TMEM44, 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-150-5P	99.99	66.69	1976
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-6716-5P	99.56	68.62	1244
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-6864-5P	98.38	66.59	1079
HSA-MIR-3179	98.22	65.90	1445
HSA-MIR-556-5P	97.75	66.17	473
HSA-MIR-1910-5P	97.42	66.36	844
HSA-MIR-6802-3P	97.29	65.42	613
HSA-MIR-4701-5P	96.45	68.41	1121
HSA-MIR-588	96.45	68.36	1127
HSA-MIR-4323	93.93	63.89	656

Literature-anchored findings (GeneRIF, showing 1)

• TMEM44 as a Novel Prognostic Marker for Kidney Renal Clear Cell Carcinoma is Associated with Tumor Invasion, Migration and Immune Infiltration. (PMID:37561335)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem44	ENSDARG00000068193
mus_musculus	Tmem44	ENSMUSG00000022537
rattus_norvegicus	Tmem44	ENSRNOG00000001726
caenorhabditis_elegans		WBGENE00021546

Paralogs (1): SLC66A1 (ENSG00000040487)

Protein

Protein identifiers

Transmembrane protein 44 — Q2T9K0 (reviewed: Q2T9K0)

All UniProt accessions (7): Q2T9K0, C9IZ85, F8WCY1, F8WE47, H7C3X7, J3KQW3, Q6PL43

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (5)

UniProt ID	Names	Canonical?
Q2T9K0-1	1	yes
Q2T9K0-2	2
Q2T9K0-4	3
Q2T9K0-6	4
Q2T9K0-7	5

RefSeq proteins (4): NP_001011655, NP_001159777, NP_001159778, NP_612408 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051415	LAAT-1	Family

UniProt features (28 total): topological domain 8, transmembrane region 7, splice variant 5, sequence variant 3, compositionally biased region 2, chain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2T9K0-F1	59.11	0.04

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): 465

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, ROZANOV_MMP14_TARGETS_UP, GOBP_AMINO_ACID_TRANSPORT, GOBP_BASIC_AMINO_ACID_TRANSPORT, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, LIU_SMARCA4_TARGETS, GOBP_TRANSMEMBRANE_TRANSPORT, GOMF_AMINO_ACID_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_TRANSPORTER_ACTIVITY, STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN, HOELZEL_NF1_TARGETS_DN, WIERENGA_STAT5A_TARGETS_DN, MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP

GO Biological Process (1): basic amino acid transmembrane transport (GO:1990822)

GO Molecular Function (2): basic amino acid transmembrane transporter activity (GO:0015174), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
amino acid transmembrane transport	1
basic amino acid transport	1
amino acid transmembrane transporter activity	1
basic amino acid transmembrane transport	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

328 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM44	LSG1	Q9H089	545
TMEM44	PPP1R18	Q6NYC8	517
TMEM44	FAM43A	Q8N2R8	505
TMEM44	CALHM2	Q9HA72	496
TMEM44	ATP13A3	Q9H7F0	479
TMEM44	FAM86B1	Q8N7N1	474
TMEM44	ANO7	Q6IWH7	462
TMEM44	C1orf226	A1L170	417
TMEM44	MCTP1	Q6DN14	416
TMEM44	SNRNP48	Q6IEG0	413
TMEM44	RUFY4	Q6ZNE9	402
TMEM44	PKD1L3	Q7Z443	377
TMEM44	FAM174C	Q9BVV8	370
TMEM44	ZNG1A	Q9BRT8	368
TMEM44	SV2B	Q7L1I2	366

IntAct

5 interactions, top by confidence:

A	B	Type	Score
GSK3B	TMEM44	psi-mi:“MI:0915”(physical association)	0.370
GEMIN6	GEMIN2	psi-mi:“MI:0914”(association)	0.350
TMEM44	SPAG9	psi-mi:“MI:0914”(association)	0.350
TMEM44	COL1A1	psi-mi:“MI:0914”(association)	0.350

BioGRID (22): SPAG9 (Affinity Capture-MS), TNKS (Affinity Capture-MS), TMEM44 (Reconstituted Complex), TMEM44 (Two-hybrid), TMEM44 (Two-hybrid), TMEM31 (Two-hybrid), CLDN7 (Two-hybrid), TMEM44 (Affinity Capture-RNA), TNKS (Affinity Capture-MS), SPAG9 (Affinity Capture-MS), TMEM44 (Affinity Capture-MS), KLHL9 (Affinity Capture-MS), COL1A2 (Affinity Capture-MS), KLHL13 (Affinity Capture-MS), COL1A1 (Affinity Capture-MS)

ESM2 similar proteins: A2A6C4, A4D0V7, A6H684, A6NH21, A7VL23, A8WCG0, E9PY61, O70397, O73698, O75631, P0C8N6, P38574, P49653, P97678, Q15904, Q16558, Q1HG43, Q28067, Q28266, Q28705, Q2T9K0, Q2YDJ2, Q498W5, Q52LC2, Q5R8Q2, Q5XK03, Q5ZJY9, Q60409, Q6P5F7, Q6PRD1, Q811Q0, Q86XJ0, Q8CAE3, Q8CB65, Q8CIP5, Q8CJ26, Q8IUH8, Q8K3P1, Q8K5A9, Q8VE49

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	86
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2031 predictions. Top by Δscore:

Variant	Effect	Δscore
3:194588636:CCCA:C	acceptor_gain	1.0000
3:194588637:CCA:C	acceptor_gain	1.0000
3:194588637:CCAC:C	acceptor_gain	1.0000
3:194588638:CA:C	acceptor_gain	1.0000
3:194588638:CAC:C	acceptor_gain	1.0000
3:194588640:C:CC	acceptor_gain	1.0000
3:194604288:T:TA	donor_gain	1.0000
3:194611022:T:C	acceptor_gain	1.0000
3:194611028:G:C	acceptor_gain	1.0000
3:194611028:G:GC	acceptor_gain	1.0000
3:194611035:C:CT	acceptor_gain	1.0000
3:194623223:CAATT:C	donor_gain	1.0000
3:194633077:A:AC	donor_gain	1.0000
3:194633078:C:CC	donor_gain	1.0000
3:194633078:CAGCG:C	donor_gain	1.0000
3:194588635:TCCCA:T	acceptor_gain	0.9900
3:194588636:CCCAC:C	acceptor_gain	0.9900
3:194588640:C:T	acceptor_loss	0.9900
3:194588642:A:C	acceptor_gain	0.9900
3:194604281:GTGTA:G	donor_loss	0.9900
3:194604282:TGTAC:T	donor_loss	0.9900
3:194604283:GTAC:G	donor_loss	0.9900
3:194604286:C:CG	donor_loss	0.9900
3:194611022:T:TC	acceptor_gain	0.9900
3:194611025:CAAG:C	acceptor_gain	0.9900
3:194611036:A:T	acceptor_gain	0.9900
3:194623222:A:AC	donor_gain	0.9900
3:194623223:C:CC	donor_gain	0.9900
3:194625923:CAGA:C	acceptor_gain	0.9900
3:194625927:C:CC	acceptor_gain	0.9900

AlphaMissense

2743 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:194617140:A:G	W295R	0.994
3:194617140:A:T	W295R	0.994
3:194633119:A:G	W33R	0.993
3:194633119:A:T	W33R	0.993
3:194628431:A:C	S72R	0.990
3:194628431:A:T	S72R	0.990
3:194628433:T:G	S72R	0.990
3:194617106:T:A	D306V	0.986
3:194617107:C:G	D306H	0.984
3:194623622:G:C	S144R	0.984
3:194623622:G:T	S144R	0.984
3:194623624:T:G	S144R	0.984
3:194633113:A:G	C35R	0.984
3:194617106:T:G	D306A	0.983
3:194628415:C:A	G78W	0.982
3:194633101:A:G	C39R	0.982
3:194617136:A:G	F296S	0.981
3:194617138:C:A	W295C	0.981
3:194617138:C:G	W295C	0.981
3:194623256:A:G	W194R	0.981
3:194623256:A:T	W194R	0.981
3:194633126:G:C	F30L	0.981
3:194633126:G:T	F30L	0.981
3:194633128:A:G	F30L	0.981
3:194633153:G:C	F21L	0.981
3:194633153:G:T	F21L	0.981
3:194633155:A:G	F21L	0.981
3:194617196:G:T	A276D	0.980
3:194617190:G:T	A278D	0.979
3:194628415:C:G	G78R	0.979

dbSNP variants (sampled 300 via entrez): RS1000067428 (3:194592617 T>C), RS1000075936 (3:194592865 G>A), RS1000141602 (3:194626985 G>A), RS1000180390 (3:194612264 T>A), RS1000182667 (3:194607392 C>T), RS1000223661 (3:194625755 C>A), RS1000245711 (3:194612994 A>G), RS1000257443 (3:194612542 C>T), RS1000429423 (3:194617110 G>A,C), RS1000447779 (3:194618380 A>G), RS1000516375 (3:194613264 G>A), RS1000584499 (3:194611758 A>T), RS1000628910 (3:194611407 T>A), RS1000798162 (3:194618434 T>C), RS1000843067 (3:194603113 A>G)

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

68 associations (top):

Study	Trait	p-value
GCST004267_3	Blood osmolality (transformed sodium)	3.000000e-06
GCST006630_57	Diastolic blood pressure	3.000000e-17
GCST010266_4	Femoral neck bone mineral density and trunk fat mass adjusted by trunk lean mass	5.000000e-07
GCST010267_5	Trunk fat mass adjusted for trunk lean mass	1.000000e-07
GCST010796_3431	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-12
GCST010796_3432	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-11
GCST010796_3433	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-12
GCST010796_3434	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-14
GCST010796_3435	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-13
GCST010796_3436	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-12
GCST010796_3437	Electrocardiogram morphology (amplitude at temporal datapoints)	5.000000e-12
GCST010796_3438	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-11
GCST010796_3439	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-11
GCST010796_3440	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-12
GCST010796_3441	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-12
GCST010796_3442	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-11
GCST010796_3443	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-11
GCST010796_3444	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-11
GCST010796_3445	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-11
GCST010796_3446	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-11
GCST010796_3447	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-11
GCST010796_3448	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-11
GCST010796_3449	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-11
GCST010796_3450	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-11
GCST010796_3526	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-12
GCST010796_3527	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-11
GCST010796_3528	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-10
GCST010796_3529	Electrocardiogram morphology (amplitude at temporal datapoints)	5.000000e-11
GCST010796_3530	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-11
GCST010796_3531	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0007785	femoral neck bone mineral density
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	5
Aflatoxin B1	increases expression, increases methylation	3
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
Estradiol	affects cotreatment, increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
FR900359	increases phosphorylation	1
methyleugenol	increases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
aflatoxin B2	decreases methylation	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dimethylarsinous acid	decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
belinostat	decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	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
Temozolomide	decreases expression	1
Decitabine	affects expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Cadmium	decreases reaction, increases abundance, increases palmitoylation	1
Cisplatin	affects expression	1
Copper	affects binding, increases expression	1

Clinical trials (associated diseases)

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