SMIM10L2B

Summary

SMIM10L2B (small integral membrane protein 10 like 2B, HGNC:34500) is a protein-coding gene on chromosome Xq26.3, encoding Small integral membrane protein 10-like protein 2B (P0DMW5).

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001348255

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34500
Approved symbol	SMIM10L2B
Name	small integral membrane protein 10 like 2B
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Aliases	RP11-85L21.2
Ensembl gene	ENSG00000196972
Ensembl biotype	protein_coding
Entrez	644596

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000433425

RefSeq mRNA: 1 — MANE Select: NM_001348255 NM_001348255

CCDS: CCDS87780

Canonical transcript exons

ENST00000433425 — 2 exons

Exon	Start	End
ENSE00001682981	135094985	135097121
ENSE00001758951	135098033	135098712

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 91.32.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7749 / max 43.7206, expressed in 501 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200615	1.4119	436
200616	0.1860	85
200614	0.0949	52
209822	0.0607	29
200613	0.0214	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	91.32	gold quality
hypothalamus	UBERON:0001898	91.18	gold quality
frontal cortex	UBERON:0001870	90.60	gold quality
superior frontal gyrus	UBERON:0002661	90.25	gold quality
anterior cingulate cortex	UBERON:0009835	90.25	gold quality
right frontal lobe	UBERON:0002810	89.54	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.52	gold quality
cerebral cortex	UBERON:0000956	89.31	gold quality
Brodmann (1909) area 9	UBERON:0013540	88.65	gold quality
Ammon’s horn	UBERON:0001954	88.12	gold quality
temporal lobe	UBERON:0001871	88.08	gold quality
amygdala	UBERON:0001876	88.02	gold quality
adrenal tissue	UBERON:0018303	87.61	gold quality
substantia nigra	UBERON:0002038	86.52	gold quality
primary visual cortex	UBERON:0002436	85.42	gold quality
brain	UBERON:0000955	83.84	gold quality
nucleus accumbens	UBERON:0001882	83.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.89	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.24	gold quality
right atrium auricular region	UBERON:0006631	79.98	gold quality
putamen	UBERON:0001874	79.58	gold quality
cerebellar cortex	UBERON:0002129	79.52	gold quality
cerebellum	UBERON:0002037	79.51	gold quality
cerebellar hemisphere	UBERON:0002245	79.50	gold quality
caudate nucleus	UBERON:0001873	79.05	gold quality
apex of heart	UBERON:0002098	75.15	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	74.61	gold quality
heart	UBERON:0000948	73.62	gold quality
heart left ventricle	UBERON:0002084	71.98	gold quality
left ovary	UBERON:0002119	70.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.81

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim10l3	ENSDARG00000100331
mus_musculus	Smim10l2a	ENSMUSG00000054850

Paralogs (4): SMIM10L2A (ENSG00000178947), SMIM10 (ENSG00000184785), SMIM10L1 (ENSG00000256537), SMIM10L3 (ENSG00000286075)

Protein

Protein identifiers

Small integral membrane protein 10-like protein 2B — P0DMW5 (reviewed: P0DMW5)

All UniProt accessions (1): P0DMW5

RefSeq proteins (1): NP_001335184* (*=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-P0DMW5-F1	65.66	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 8 (showing top): chrXq26, SALL4_TARGET_GENES, ZNF768_TARGET_GENES, MEBARKI_HCC_PROGENITOR_FZD8CRD_DN, CUX1_TARGET_GENES, ZNF547_TARGET_GENES, GENES_CORRELATED_WITH_MN1_DELETION, GENES_CORRELATED_WITH_SOX2_DELETION

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

291 predictions. Top by Δscore:

Variant	Effect	Δscore
X:135096969:G:A	donor_gain	0.9900
X:135098029:CTAC:C	donor_loss	0.9900
X:135098030:TA:T	donor_loss	0.9900
X:135098032:C:A	donor_loss	0.9900
X:135098032:CCTTT:C	donor_gain	0.9900
X:135097119:TGC:T	acceptor_gain	0.9800
X:135098399:A:AC	donor_gain	0.9700
X:135098400:C:CC	donor_gain	0.9700
X:135098431:A:AC	donor_gain	0.9700
X:135097119:TGCC:T	acceptor_loss	0.9600
X:135097121:CCT:C	acceptor_loss	0.9600
X:135097122:C:CG	acceptor_loss	0.9600
X:135097123:T:A	acceptor_loss	0.9600
X:135096112:CAG:C	acceptor_gain	0.9500
X:135097122:C:CC	acceptor_gain	0.9500
X:135098031:A:AC	donor_gain	0.9400
X:135098032:C:CC	donor_gain	0.9400
X:135098080:T:TA	donor_gain	0.9400
X:135096295:T:C	acceptor_gain	0.9100
X:135096972:TC:T	donor_gain	0.9100
X:135096994:T:A	donor_gain	0.8900
X:135097118:ATGC:A	acceptor_gain	0.8900
X:135098414:G:A	donor_gain	0.8900
X:135097120:GC:G	acceptor_gain	0.8700
X:135097121:CC:C	acceptor_gain	0.8700
X:135097124:G:C	acceptor_loss	0.8700
X:135096944:C:A	donor_gain	0.8600
X:135096975:A:AC	donor_gain	0.8500
X:135096976:C:CC	donor_gain	0.8500
X:135097117:AATGC:A	acceptor_gain	0.8400

AlphaMissense

473 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1003389410 (X:135100387 T>C), RS1023384627 (X:135100364 T>G), RS1023925679 (X:135099911 A>C), RS1036468552 (X:135100298 T>C,G), RS1038617416 (X:135100586 A>T), RS1039782414 (X:135100136 A>G), RS1045095414 (X:135100694 G>A,T), RS1051229282 (X:135100517 T>C), RS112125662 (X:135097239 G>A), RS1135844 (X:135095351 T>C), RS1135846 (X:135095319 A>G), RS1135848 (X:135095303 G>A), RS1158419625 (X:135098493 G>T), RS1158558428 (X:135097400 G>A), RS1158595895 (X:135097889 C>CT)

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

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	2
Valproic Acid	increases expression, increases methylation	2
aristolochic acid I	decreases expression	1
propionaldehyde	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	affects expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
ferrous chloride	decreases expression	1
pentanal	increases expression	1
Grape Seed Proanthocyanidins	increases expression, affects cotreatment	1
Glyphosate	decreases expression	1
Aldehydes	increases expression	1
Catechin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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