TMEM41A

Summary

TMEM41A (transmembrane protein 41A, HGNC:30544) is a protein-coding gene on chromosome 3q27.2, encoding Transmembrane protein 41A (Q96HV5).

Predicted to be located in membrane.

Source: NCBI Gene 90407 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_080652

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30544
Approved symbol	TMEM41A
Name	transmembrane protein 41A
Location	3q27.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC15397
Ensembl gene	ENSG00000163900
Ensembl biotype	protein_coding
Entrez	90407

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000296254, ENST00000382227, ENST00000421852, ENST00000467061, ENST00000467520, ENST00000475480, ENST00000484062, ENST00000856958

RefSeq mRNA: 1 — MANE Select: NM_080652 NM_080652

CCDS: CCDS3271

Canonical transcript exons

ENST00000421852 — 5 exons

Exon	Start	End
ENSE00001079509	185498843	185499035
ENSE00001792412	185489601	185491757
ENSE00003653724	185494623	185494761
ENSE00003675562	185495154	185495315
ENSE00003675997	185496828	185496981

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 97.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.9066 / max 132.9220, expressed in 1799 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
45922	10.0591	1781
45921	4.8475	1709

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	97.65	gold quality
secondary oocyte	CL:0000655	97.46	gold quality
ileal mucosa	UBERON:0000331	95.76	gold quality
adrenal tissue	UBERON:0018303	94.68	gold quality
upper arm skin	UBERON:0004263	92.01	gold quality
right adrenal gland cortex	UBERON:0035827	91.11	gold quality
jejunal mucosa	UBERON:0000399	90.91	gold quality
left adrenal gland cortex	UBERON:0035825	90.63	gold quality
adrenal cortex	UBERON:0001235	90.61	gold quality
left adrenal gland	UBERON:0001234	90.38	gold quality
adrenal gland	UBERON:0002369	90.21	gold quality
right adrenal gland	UBERON:0001233	89.97	gold quality
lower esophagus mucosa	UBERON:0035834	89.83	gold quality
duodenum	UBERON:0002114	89.15	gold quality
esophagus mucosa	UBERON:0002469	88.32	gold quality
tibialis anterior	UBERON:0001385	88.21	silver quality
nipple	UBERON:0002030	87.94	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.89	gold quality
skin of abdomen	UBERON:0001416	87.84	gold quality
skin of leg	UBERON:0001511	87.06	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.91	gold quality
small intestine	UBERON:0002108	86.86	gold quality
zone of skin	UBERON:0000014	86.70	gold quality
lateral nuclear group of thalamus	UBERON:0002736	86.45	gold quality
kidney epithelium	UBERON:0004819	86.36	silver quality
metanephros	UBERON:0000081	86.31	gold quality
nasal cavity epithelium	UBERON:0005384	85.97	gold quality
islet of Langerhans	UBERON:0000006	85.68	gold quality
esophagus squamous epithelium	UBERON:0006920	85.64	gold quality
right lobe of liver	UBERON:0001114	85.62	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	18.83
E-GEOD-109979	no	173.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting TMEM41A, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-223-3P	99.99	70.14	1140
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-577	99.78	69.13	2479

Literature-anchored findings (GeneRIF, showing 2)

• The present study demonstrated a reduction in TMEM41A expression levels in a pair of GC cell lines, and revealed that high TMEM41A expression levels may promote GC-associated metastasis, which may be mediated by the downregulation of E-cadherin expression. (PMID:30015937)
• TMEM41A overexpression correlates with poor prognosis and immune alterations in patients with endometrial carcinoma. (PMID:37478120)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem41ab	ENSDARG00000026771
caenorhabditis_elegans	Y71A12C.2	WBGENE00013513

Paralogs (2): TMEM41B (ENSG00000166471), TMEM64 (ENSG00000180694)

Protein

Protein identifiers

Transmembrane protein 41A — Q96HV5 (reviewed: Q96HV5)

All UniProt accessions (3): Q96HV5, F8WDE2, H7BXL1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Domain organisation. The VTT domain was previously called the SNARE-assoc domain. As there is no evidence that this domain associates with SNARE proteins, it was renamed as VMP1, TMEM41, and TVP38 (VTT) domain.

Similarity. Belongs to the TMEM41 family.

RefSeq proteins (1): NP_542383* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032816	VTT_dom	Domain
IPR045014	TM41A/B	Family

Pfam: PF09335

UniProt features (9 total): transmembrane region 5, signal peptide 1, chain 1, region of interest 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96HV5-F1	84.38	0.49

Functional residue map

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

Glycosylation sites (1): 250

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 145 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP, SENESE_HDAC1_TARGETS_UP, DOUGLAS_BMI1_TARGETS_UP, NUYTTEN_EZH2_TARGETS_DN, LEIN_CEREBELLUM_MARKERS, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, BRUINS_UVC_RESPONSE_MIDDLE, KASLER_HDAC7_TARGETS_1_UP, LIM_MAMMARY_STEM_CELL_DN, GSE14415_FOXP3_KO_NATURAL_TREG_VS_TCONV_DN, GSE5503_PLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_UP

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

760 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TMEM41A	TMPPE	Q6ZT21	589
TMEM41A	SLC66A3	Q8N755	558
TMEM41A	SPRING1	Q9H741	538
TMEM41A	TMEM109	Q9BVC6	526
TMEM41A	TMEM126A	Q9H061	509
TMEM41A	TMEM64	Q6YI46	491
TMEM41A	VMP1	Q96GC9	482
TMEM41A	SEC11C	Q9BY50	476
TMEM41A	OR2A14	Q96R47	458
TMEM41A	AGPS	O00116	446
TMEM41A	STT3A	P46977	441
TMEM41A	FAM162B	Q5T6X4	410
TMEM41A	MBTPS1	Q14703	405
TMEM41A	UNC50	Q53HI1	398
TMEM41A	UBIAD1	Q9Y5Z9	394

IntAct

35 interactions, top by confidence:

A	B	Type	Score
TMEM41A	NOTCH2NLA	psi-mi:“MI:0915”(physical association)	0.560
TMEM41A	KASH5	psi-mi:“MI:0915”(physical association)	0.560
KASH5	TMEM41A	psi-mi:“MI:0915”(physical association)	0.560
LPAR3	TMEM41A	psi-mi:“MI:0915”(physical association)	0.560
TMEM41A	LPAR3	psi-mi:“MI:0915”(physical association)	0.560
FA2H	TMEM41A	psi-mi:“MI:0915”(physical association)	0.560
	TMEM41A	psi-mi:“MI:0915”(physical association)	0.560
CYB5B	TMEM41A	psi-mi:“MI:0915”(physical association)	0.560
STX1A	TMEM41A	psi-mi:“MI:0915”(physical association)	0.560
PTPN1	TMEM41A	psi-mi:“MI:0915”(physical association)	0.560
TMEM41A	rep	psi-mi:“MI:0915”(physical association)	0.550
APP	MGST3	psi-mi:“MI:0914”(association)	0.350
VIPR2	C15orf61	psi-mi:“MI:0914”(association)	0.350
rep	GPR89A	psi-mi:“MI:0914”(association)	0.350
M	DENND11	psi-mi:“MI:0914”(association)	0.350
BSCL2	TMEM223	psi-mi:“MI:0914”(association)	0.350
MFSD5	ILVBL	psi-mi:“MI:0914”(association)	0.350
SLC19A2	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLC7A4	ESYT2	psi-mi:“MI:0914”(association)	0.350
TCTN3	TMEM120B	psi-mi:“MI:2364”(proximity)	0.270
TMEM41A	STX1A	psi-mi:“MI:0915”(physical association)	0.000
	TMEM41A	psi-mi:“MI:0915”(physical association)	0.000
CYB5B	TMEM41A	psi-mi:“MI:0915”(physical association)	0.000
FA2H	TMEM41A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (29): CCDC155 (Two-hybrid), NOTCH2NL (Two-hybrid), TMEM41A (Proximity Label-MS), TMEM41A (Affinity Capture-MS), TMEM41A (Two-hybrid), TMEM41A (Affinity Capture-MS), TMEM41A (Two-hybrid), TMEM41A (Two-hybrid), TMEM41A (Two-hybrid), LPAR3 (Two-hybrid), PTPN1 (Two-hybrid), FXYD6-FXYD2 (Two-hybrid), TMEM41A (Affinity Capture-MS), TMEM41A (Affinity Capture-MS), TMEM41A (Affinity Capture-MS)

ESM2 similar proteins: A6NFX1, B0BMY1, D2HKB0, D3ZG27, D3ZH22, E7FB98, F1NJ67, O00219, P59266, Q17QZ3, Q1LZA0, Q28727, Q3T9M1, Q3UMZ3, Q4R581, Q5EAL3, Q5EB14, Q5R9A1, Q5RA57, Q5ZJX0, Q5ZKS8, Q60441, Q66H95, Q68F72, Q6AY78, Q6NTJ7, Q6ZP29, Q8BFQ6, Q8C4N4, Q8C6U2, Q8L9J7, Q8N755, Q8NEB5, Q8TB61, Q8TBR7, Q91W98, Q91WC7, Q91ZN5, Q92521, Q95KW8

Diamond homologs: A1A5V7, A4II98, O62126, Q08D99, Q502G2, Q5BJD5, Q5FVN2, Q5RBZ8, Q5U4K5, Q5ZIL6, Q6NV38, Q8K1A5, Q8L586, Q8MXN7, Q96HV5, Q9D8U2, Q9VX39

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

959 predictions. Top by Δscore:

Variant	Effect	Δscore
3:185477325:GA:G	acceptor_gain	1.0000
3:185480223:T:A	acceptor_gain	1.0000
3:185480230:A:AG	acceptor_gain	1.0000
3:185480231:G:GC	acceptor_loss	1.0000
3:185480231:G:GG	acceptor_gain	1.0000
3:185480499:C:T	donor_gain	1.0000
3:185480516:A:T	donor_gain	1.0000
3:185480528:AGGTG:A	donor_loss	1.0000
3:185480529:GGTG:G	donor_loss	1.0000
3:185480530:G:C	donor_loss	1.0000
3:185482350:TGCA:T	acceptor_loss	1.0000
3:185482351:GCA:G	acceptor_loss	1.0000
3:185482353:A:AG	acceptor_gain	1.0000
3:185482353:A:G	acceptor_loss	1.0000
3:185482354:G:GC	acceptor_gain	1.0000
3:185482354:GA:G	acceptor_gain	1.0000
3:185482354:GAA:G	acceptor_gain	1.0000
3:185482354:GAAC:G	acceptor_gain	1.0000
3:185496824:TGACC:T	donor_loss	1.0000
3:185496825:GACCA:G	donor_loss	1.0000
3:185496826:A:AC	donor_gain	1.0000
3:185496826:ACCAG:A	donor_loss	1.0000
3:185496827:C:CC	donor_gain	1.0000
3:185496899:AGG:A	donor_gain	1.0000
3:185496978:CGAC:C	acceptor_gain	1.0000
3:185496981:CCT:C	acceptor_loss	1.0000
3:185496982:C:CC	acceptor_gain	1.0000
3:185496983:T:G	acceptor_loss	1.0000
3:185496989:T:TC	acceptor_gain	1.0000
3:185496990:T:C	acceptor_gain	1.0000

AlphaMissense

1690 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:185491721:C:T	G204E	0.998
3:185491741:A:C	N197K	0.998
3:185491741:A:T	N197K	0.998
3:185494623:C:G	G192R	0.998
3:185495265:G:C	C108W	0.998
3:185491637:G:T	A232E	0.997
3:185491646:G:T	A229D	0.997
3:185491722:C:A	G204W	0.997
3:185491757:C:T	G192D	0.997
3:185494681:G:C	N172K	0.997
3:185494681:G:T	N172K	0.997
3:185494692:A:G	W169R	0.997
3:185494692:A:T	W169R	0.997
3:185494715:C:G	R161T	0.997
3:185495245:C:T	G115D	0.997
3:185495279:C:A	G104W	0.997
3:185495302:C:T	G96D	0.997
3:185495313:A:C	N92K	0.997
3:185495313:A:T	N92K	0.997
3:185496834:G:C	S89R	0.997
3:185496834:G:T	S89R	0.997
3:185496836:T:G	S89R	0.997
3:185496861:T:A	K80N	0.997
3:185496861:T:G	K80N	0.997
3:185491722:C:G	G204R	0.996
3:185491722:C:T	G204R	0.996
3:185495246:C:G	G115R	0.996
3:185495266:C:T	C108Y	0.996
3:185495279:C:G	G104R	0.996
3:185495279:C:T	G104R	0.996

dbSNP variants (sampled 300 via entrez): RS1000079100 (3:185494642 G>A,C), RS1000151136 (3:185494148 A>C), RS1000213414 (3:185500516 T>C), RS1000424686 (3:185494464 C>T), RS1001089389 (3:185496066 G>T), RS1001311934 (3:185490881 G>T), RS1001642698 (3:185499648 A>G), RS1001884675 (3:185499338 A>G), RS1002160244 (3:185492820 C>G,T), RS1002535396 (3:185498717 A>G,T), RS1002547561 (3:185496448 T>C), RS1002987179 (3:185492283 T>C), RS1003641447 (3:185491425 T>C), RS1003708887 (3:185490562 T>C,G), RS1003773329 (3:185497346 T>C)

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

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases expression	4
bisphenol A	increases expression, affects cotreatment	2
Acetaminophen	increases expression	2
Tetrachlorodibenzodioxin	increases expression	2
Tobacco Smoke Pollution	increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
terbufos	decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases abundance, increases expression, affects cotreatment	1
perfluorooctanoic acid	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
ICG 001	increases expression	1
abrine	decreases expression	1
Rosiglitazone	decreases expression	1
Sunitinib	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Fonofos	decreases methylation	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Parathion	decreases methylation	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1

Clinical trials (associated diseases)

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