SMIM10L2A

Summary

SMIM10L2A (small integral membrane protein 10 like 2A, HGNC:34499) is a protein-coding gene on chromosome Xq26.3, encoding Small integral membrane protein 10-like protein 2A (P0DMW4).

This gene encodes a highly conserved small protein that contains a conserved motif (DUF4560) and may function as an integral membrane protein. This transcript was also shown to associate with enhancer chromatin and therefore may also function as an RNA to regulate enhancers.

Source: NCBI Gene 399668 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_203306

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34499
Approved symbol	SMIM10L2A
Name	small integral membrane protein 10 like 2A
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC39606, LED, LINC0086
Ensembl gene	ENSG00000178947
Ensembl biotype	protein_coding
Entrez	399668

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000417443

RefSeq mRNA: 1 — MANE Select: NM_203306 NM_203306

Canonical transcript exons

ENST00000417443 — 2 exons

Exon	Start	End
ENSE00001248437	135421944	135422730
ENSE00001634729	135423633	135428075

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 92.59.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0388 / max 61.9804, expressed in 425 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197635	0.8775	258
197633	0.8641	310
197634	0.2715	152
209823	0.0257	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	92.59	gold quality
right adrenal gland cortex	UBERON:0035827	91.42	gold quality
anterior cingulate cortex	UBERON:0009835	90.55	gold quality
right adrenal gland	UBERON:0001233	90.23	gold quality
prefrontal cortex	UBERON:0000451	90.11	gold quality
left adrenal gland cortex	UBERON:0035825	89.14	gold quality
adrenal cortex	UBERON:0001235	88.90	gold quality
left adrenal gland	UBERON:0001234	88.89	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.73	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.59	gold quality
frontal cortex	UBERON:0001870	88.31	gold quality
amygdala	UBERON:0001876	88.20	gold quality
right frontal lobe	UBERON:0002810	88.12	gold quality
hypothalamus	UBERON:0001898	88.10	gold quality
neocortex	UBERON:0001950	88.10	gold quality
adrenal gland	UBERON:0002369	87.55	gold quality
Ammon’s horn	UBERON:0001954	87.45	gold quality
cerebral cortex	UBERON:0000956	87.36	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.31	gold quality
temporal lobe	UBERON:0001871	86.37	gold quality
nucleus accumbens	UBERON:0001882	86.29	gold quality
Brodmann (1909) area 46	UBERON:0006483	85.77	gold quality
superior frontal gyrus	UBERON:0002661	85.74	gold quality
entorhinal cortex	UBERON:0002728	85.00	gold quality
caudate nucleus	UBERON:0001873	84.61	gold quality
primary visual cortex	UBERON:0002436	84.39	gold quality
forebrain	UBERON:0001890	84.18	gold quality
putamen	UBERON:0001874	84.17	gold quality
middle temporal gyrus	UBERON:0002771	83.87	gold quality
brain	UBERON:0000955	82.69	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-8060	no	67.01
E-ANND-3	no	2.04

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• tumor-suppressive role of LINC0086 in NPC. Low expression of LINC0086 is associated with a poor prognosis of NPC patients. Upregulation of LINC0086 significantly inhibited NPC cancer cell growth and caused apoptosis in vitro and in vivo by targeting miR-214. (PMID:28245169)
• Plasma long noncoding RNA LINC00086 expression is significantly lower in gastric cancer (GC) patients than in normal individuals. GC patients with low LINC00086 expression are likely to have larger tumors, lymphatic metastasis, larger TNM stage, and higher carcinoembryonic antigen and carbohydrate antigen 19-9 levels. GC patients with low LINC00086 expression show lower survival rates. (PMID:30689553)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim10l3	ENSDARG00000100331
mus_musculus	Smim10l2a	ENSMUSG00000054850

Paralogs (4): SMIM10 (ENSG00000184785), SMIM10L2B (ENSG00000196972), SMIM10L1 (ENSG00000256537), SMIM10L3 (ENSG00000286075)

Protein

Protein identifiers

Small integral membrane protein 10-like protein 2A — P0DMW4 (reviewed: P0DMW4)

All UniProt accessions (1): P0DMW4

RefSeq proteins (1): NP_976051* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029367	SMIM10	Family

Pfam: PF15118

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DMW4-F1	67.79	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, chrXq26, ZNF618_TARGET_GENES, DESCARTES_MAIN_FETAL_SLC26A4_PAEP_POSITIVE_CELLS, NKX2_5_TARGET_GENES, ZNF740_TARGET_GENES, HARALAMBIEVA_PBMC_M_M_R_II_AGE_11_22YO_VACCINATED_VS_UNVACCINATED_7YR_DN, PEREZ_TP53_TARGETS, ACCTGTTG_UNKNOWN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

94 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM10L2A	DIP2C-AS1	Q8N8Z3	507
SMIM10L2A	CCDC163	A0A0D9SF12	506
SMIM10L2A	SMIM21	Q3B7S5	476
SMIM10L2A	AQP12B	A6NM10	445
SMIM10L2A	ZSCAN23	Q3MJ62	419
SMIM10L2A	SERHL2	Q9H4I8	402
SMIM10L2A	TMEM187	Q14656	380
SMIM10L2A	PCDHGB6	Q9Y5F9	349
SMIM10L2A	GPR52	Q9Y2T5	348
SMIM10L2A	FIBCD1	Q8N539	336
SMIM10L2A	DIRAS1	O95057	331
SMIM10L2A	JMJD4	Q9H9V9	323
SMIM10L2A	PPP1R14B	Q96C90	317
SMIM10L2A	RPL22L1	Q6P5R6	289
SMIM10L2A	KIF26B	Q2KJY2	271

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A023PXF2, A0A0C4DGP1, A0LE50, B2JJR9, B2T7U2, B7GPF6, C0H3T2, G2TRK6, O13517, O29555, O83098, O83173, O83253, O83740, O83788, P0C272, P0C5Q1, P0DMW4, P0DMW5, P0DQF8, P0DQM5, P0DXX6, P11189, P16777, P23985, P29069, P41669, P41953, P76023, Q05102, Q05381, Q0Q043, Q12130, Q12506, Q13SH3, Q28UQ5, Q2Y5A7, Q32063, Q3E7A0, Q3V4W8

Diamond homologs: A0A0C4DGP1, P0DMW3, P0DMW4, P0DMW5, Q5U425, Q96HG1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

445 predictions. Top by Δscore:

Variant	Effect	Δscore
X:135422453:A:T	donor_gain	0.9800
X:135422726:GAAAG:G	donor_gain	0.9800
X:135422727:AAAG:A	donor_loss	0.9800
X:135422728:AAG:A	donor_loss	0.9800
X:135422729:AGG:A	donor_loss	0.9800
X:135422730:GGT:G	donor_loss	0.9800
X:135422731:G:GA	donor_loss	0.9800
X:135422732:T:G	donor_loss	0.9800
X:135423786:C:T	donor_gain	0.9700
X:135424640:ACT:A	acceptor_gain	0.9200
X:135422333:A:AG	donor_gain	0.9000
X:135423850:A:T	donor_gain	0.9000
X:135423853:GTC:G	donor_gain	0.9000
X:135423854:TCT:T	donor_gain	0.9000
X:135423849:G:GT	donor_gain	0.8900
X:135422365:G:GG	donor_gain	0.8800
X:135422452:G:GT	donor_gain	0.8800
X:135422364:A:AG	donor_gain	0.8600
X:135427136:A:AG	acceptor_gain	0.8600
X:135427137:G:GG	acceptor_gain	0.8600
X:135422731:G:GG	donor_gain	0.8300
X:135423781:AG:A	donor_gain	0.8100
X:135427137:GA:G	acceptor_gain	0.8100
X:135425167:C:G	donor_gain	0.8000
X:135427063:C:T	donor_gain	0.7900
X:135423820:GCCC:G	donor_gain	0.7800
X:135426793:G:GT	donor_gain	0.7800
X:135424592:G:GT	donor_gain	0.7600
X:135425156:A:T	donor_gain	0.7500
X:135426883:C:T	donor_gain	0.7500

AlphaMissense

472 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:135422237:T:C	F36L	0.982
X:135422239:C:A	F36L	0.982
X:135422239:C:G	F36L	0.982
X:135422273:T:C	F48L	0.977
X:135422275:C:A	F48L	0.977
X:135422275:C:G	F48L	0.977
X:135422283:C:A	A51D	0.972
X:135422250:T:A	L40H	0.971
X:135422325:C:A	A65D	0.970
X:135422303:T:C	F58L	0.964
X:135422305:C:A	F58L	0.964
X:135422305:C:G	F58L	0.964
X:135422304:T:C	F58S	0.960
X:135422304:T:G	F58C	0.955
X:135422343:T:A	V71D	0.954
X:135422287:G:C	W52C	0.950
X:135422287:G:T	W52C	0.950
X:135422273:T:A	F48I	0.945
X:135422245:G:C	K38N	0.944
X:135422245:G:T	K38N	0.944
X:135422349:T:C	L73P	0.944
X:135422238:T:G	F36C	0.942
X:135422327:T:C	S66P	0.942
X:135422262:T:C	L44P	0.940
X:135422285:T:A	W52R	0.940
X:135422285:T:C	W52R	0.940
X:135422280:T:C	L50P	0.939
X:135422238:T:C	F36S	0.938
X:135422253:C:A	T41K	0.934
X:135422334:T:G	M68R	0.934

dbSNP variants (sampled 300 via entrez): RS1005711872 (X:135420421 C>T), RS1005911945 (X:135420059 C>T), RS1010718031 (X:135427952 G>C), RS1011838468 (X:135420535 G>C), RS1012389729 (X:135427826 G>T), RS1015999340 (X:135420093 T>G), RS1018140150 (X:135427990 A>T), RS1018236606 (X:135428543 A>G), RS1024858703 (X:135420192 T>G), RS1025078954 (X:135420541 C>T), RS1026247966 (X:135420011 G>C), RS1030123831 (X:135428565 A>T), RS1030952136 (X:135420636 A>G), RS1041453837 (X:135420388 T>C), RS1046175612 (X:135427827 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

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	decreases expression	1
2-palmitoylglycerol	increases expression	1
1-hydroxy-1-norresistomycin	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	1
Benzo(a)pyrene	affects methylation	1
Catechin	affects cotreatment, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, decreases expression	1
Fluorouracil	decreases expression	1
Niclosamide	increases expression	1
Tobacco Smoke Pollution	affects expression	1
1-Methyl-4-phenylpyridinium	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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