SMIM10L3

Summary

SMIM10L3 (small integral membrane protein 10 like 3, HGNC:56768) is a protein-coding gene on chromosome 7p22.1, encoding Small integral membrane protein 10-like protein 3 (A0A0C4DGP1). It is a selective cancer dependency (DepMap: 25.0% of cell lines).

At a glance

• Clinical variants (ClinVar): 1 total
• Cancer dependency (DepMap): dependent in 25.0% of screened cell lines
• MANE Select transcript: NM_001395995

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:56768
Approved symbol	SMIM10L3
Name	small integral membrane protein 10 like 3
Location	7p22.1
Locus type	gene with protein product
Status	Approved
Aliases	SAGSIN1
Ensembl gene	ENSG00000286075
Ensembl biotype	protein_coding
Entrez	122526779

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000578372

RefSeq mRNA: 1 — MANE Select: NM_001395995 NM_001395995

CCDS: CCDS94053

Canonical transcript exons

ENST00000578372 — 2 exons

Exon	Start	End
ENSE00003978167	6329411	6331235
ENSE00003978168	6348573	6348967

Expression profiles

Bgee: expression breadth broad, 43 present calls, max score 44.97.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	44.97	gold quality
duodenum	UBERON:0002114	38.68	gold quality
ganglionic eminence	UBERON:0004023	38.53	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
bone marrow	UBERON:0002371	36.51	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
right uterine tube	UBERON:0001302	35.78	gold quality
blood	UBERON:0000178	35.52	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
vermiform appendix	UBERON:0001154	33.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
liver	UBERON:0002107	31.37	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
tonsil	UBERON:0002372	30.43	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
kidney	UBERON:0002113	28.73	gold quality
lymph node	UBERON:0000029	27.57	gold quality
adult mammalian kidney	UBERON:0000082	27.52	gold quality
urinary bladder	UBERON:0001255	27.32	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
cortex of kidney	UBERON:0001225	26.06	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
pancreas	UBERON:0001264	24.86	gold quality
leukocyte	CL:0000738	24.80	gold quality
muscle of leg	UBERON:0001383	24.79	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 25.0% of screened cell lines.

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim10l3	ENSDARG00000100331
mus_musculus	Smim10l3	ENSMUSG00000118332

Paralogs (4): SMIM10L2A (ENSG00000178947), SMIM10 (ENSG00000184785), SMIM10L2B (ENSG00000196972), SMIM10L1 (ENSG00000256537)

Protein

Protein identifiers

Small integral membrane protein 10-like protein 3 — A0A0C4DGP1 (reviewed: A0A0C4DGP1)

Alternative names: Salivary gland-specific protein SAGSIN1

All UniProt accessions (1): A0A0C4DGP1

RefSeq proteins (1): NP_001382924* (*=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-A0A0C4DGP1-F1	67.90	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr7p22

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, A6X974, C0QIZ2, I2HB70, O30141, O60756, P05678, P0C5L6, P0DQF8, P0DXX6, P11304, P17142, P34249, P36153, P38470, P38726, P39550, P39566, P40326, P40365, P40521, P40551, P40575, P40895, P47020, P53056, P54949, P59471, P87264, P92534, P93284, P93302, Q02918, Q03913, Q04909, Q12506, Q3E7Z1, Q5QFB9

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	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

213 predictions. Top by Δscore:

Variant	Effect	Δscore
7:6348569:CCA:C	donor_loss	1.0000
7:6348570:CA:C	donor_loss	1.0000
7:6348571:A:AG	donor_loss	1.0000
7:6348572:CCT:C	donor_loss	1.0000
7:6348568:CCCA:C	donor_gain	0.9800
7:6348477:G:C	donor_gain	0.9600
7:6348571:A:AC	donor_gain	0.9600
7:6348572:C:CC	donor_gain	0.9600
7:6348634:AGCCG:A	donor_gain	0.9600
7:6338993:A:AC	donor_gain	0.9500
7:6338994:C:CC	donor_gain	0.9500
7:6338994:CTGTG:C	donor_gain	0.9400
7:6348572:CCTG:C	donor_gain	0.9400
7:6348634:AG:A	donor_gain	0.9400
7:6344051:A:T	donor_gain	0.9300
7:6348411:C:CT	donor_gain	0.9200
7:6348569:CCACC:C	donor_gain	0.9200
7:6348635:G:C	donor_gain	0.9200
7:6348471:CA:C	donor_gain	0.9100
7:6348571:ACC:A	donor_gain	0.9100
7:6348570:CAC:C	donor_gain	0.9000
7:6348572:C:CT	donor_gain	0.9000
7:6338989:A:C	donor_gain	0.8900
7:6344052:A:AC	donor_gain	0.8900
7:6344053:C:CC	donor_gain	0.8900
7:6348412:C:CT	donor_gain	0.8900
7:6344054:T:C	donor_gain	0.8800
7:6348573:C:T	donor_gain	0.8800
7:6332108:TCACG:T	acceptor_gain	0.8500
7:6348560:ACGG:A	donor_gain	0.8500

AlphaMissense

424 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:6348651:G:C	F36L	0.991
7:6348651:G:T	F36L	0.991
7:6348653:A:G	F36L	0.991
7:6348673:G:A	T29I	0.991
7:6348621:G:C	F46L	0.990
7:6348621:G:T	F46L	0.990
7:6348623:A:G	F46L	0.990
7:6348687:G:C	F24L	0.990
7:6348687:G:T	F24L	0.990
7:6348689:A:G	F24L	0.990
7:6348577:A:G	L61P	0.989
7:6348622:A:G	F46S	0.989
7:6348622:A:C	F46C	0.988
7:6348643:G:T	A39D	0.987
7:6348598:G:A	S54F	0.986
7:6348601:G:T	A53D	0.986
7:6348598:G:T	S54Y	0.983
7:6348599:A:G	S54P	0.981
7:6348646:A:G	L38P	0.981
7:6348664:A:G	L32P	0.980
7:6348653:A:T	F36I	0.979
7:6348639:C:A	W40C	0.978
7:6348639:C:G	W40C	0.978
7:6348664:A:T	L32Q	0.978
7:6348592:A:C	M56R	0.974
7:6348607:A:T	I51N	0.974
7:6348611:A:G	Y50H	0.974
7:6348619:G:T	P47H	0.974
7:6348583:A:T	V59D	0.973
7:6348604:A:T	V52E	0.973

dbSNP variants (sampled 300 via entrez): RS1000065705 (7:6339876 G>A,T), RS1000137293 (7:6348798 T>C), RS1000416847 (7:6340009 T>C), RS1000483518 (7:6332952 A>G), RS1000717823 (7:6347526 AAAAG>A), RS1000768632 (7:6331360 A>C,G), RS1000803810 (7:6346798 T>C), RS1000890663 (7:6343042 AAAAAAAG>A), RS1000947128 (7:6347960 G>C), RS1000948224 (7:6329240 G>A,T), RS1001064540 (7:6347824 T>C), RS1001212996 (7:6333425 G>C), RS1001321435 (7:6330557 G>A,C), RS1001515512 (7:6338493 G>C,T), RS1001560003 (7:6345116 CTTG>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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance	1
Smoke	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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