SMIM48

Summary

SMIM48 (small integral membrane protein 48, HGNC:58752) is a protein-coding gene on chromosome 17p13.2, encoding Small integral membrane protein 48 (A0A494C1I1).

At a glance

• MANE Select transcript: NM_001162371

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:58752
Approved symbol	SMIM48
Name	small integral membrane protein 48
Location	17p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000286190
Ensembl biotype	protein_coding
Entrez	728392

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000568641, ENST00000956689

RefSeq mRNA: 1 — MANE Select: NM_001162371 NM_001162371

CCDS: CCDS92238

Canonical transcript exons

ENST00000568641 — 2 exons

Exon	Start	End
ENSE00002598714	5499427	5499950
ENSE00002615845	5500031	5501006

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 99.41.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pituitary gland	UBERON:0000007	99.41	gold quality
adenohypophysis	UBERON:0002196	99.40	gold quality
hypothalamus	UBERON:0001898	99.12	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.84	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.83	gold quality
anterior cingulate cortex	UBERON:0009835	98.79	gold quality
superior frontal gyrus	UBERON:0002661	98.78	gold quality
temporal lobe	UBERON:0001871	98.71	gold quality
amygdala	UBERON:0001876	98.71	gold quality
prefrontal cortex	UBERON:0000451	98.64	gold quality
cerebral cortex	UBERON:0000956	98.63	gold quality
frontal cortex	UBERON:0001870	98.59	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.59	gold quality
right frontal lobe	UBERON:0002810	98.53	gold quality
nucleus accumbens	UBERON:0001882	98.52	gold quality
Ammon’s horn	UBERON:0001954	98.50	gold quality
primary visual cortex	UBERON:0002436	98.22	gold quality
substantia nigra	UBERON:0002038	98.14	gold quality
caudate nucleus	UBERON:0001873	97.99	gold quality
putamen	UBERON:0001874	97.79	gold quality
brain	UBERON:0000955	97.75	gold quality
cortical plate	UBERON:0005343	97.75	gold quality
ganglionic eminence	UBERON:0004023	96.28	gold quality
ventricular zone	UBERON:0003053	95.16	gold quality
granulocyte	CL:0000094	94.58	gold quality
right uterine tube	UBERON:0001302	94.58	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.66	gold quality
islet of Langerhans	UBERON:0000006	93.56	gold quality
cerebellum	UBERON:0002037	93.43	gold quality
cerebellar cortex	UBERON:0002129	93.41	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	803.06
E-MTAB-5061	yes	293.51
E-GEOD-81608	no	4.80
E-GEOD-99795	no	4.50
E-ANND-3	no	2.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting SMIM48, 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-5692A	100.00	74.40	6850
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-149-5P	99.25	67.16	1315
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-3179	98.22	65.90	1445
HSA-MIR-6870-3P	98.08	65.10	692
HSA-MIR-4275	97.96	68.42	1549
HSA-MIR-924	97.78	66.21	681
HSA-MIR-7112-3P	97.67	68.77	948
HSA-MIR-5196-3P	97.57	65.98	979
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-8081	96.42	67.75	738
HSA-MIR-627-5P	95.51	66.80	509

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	6330403K07Rik	ENSMUSG00000018451
rattus_norvegicus	6330403K07Rikl	ENSRNOG00000059827

Protein

Protein identifiers

Small integral membrane protein 48 — A0A494C1I1 (reviewed: A0A494C1I1)

All UniProt accessions (1): A0A494C1I1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Endoplasmic reticulum membrane.

RefSeq proteins (1): NP_001155843* (*=MANE)

Domains & families (InterPro)

UniProt features (4 total): topological domain 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for A0A494C1I1 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

2 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM48	PRSS56	P0CW18	178

IntAct

0 interactions, top by confidence:

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

0 predictions. Top by Δscore:

AlphaMissense

758 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:5500649:G:T	A103D	0.983
17:5500652:A:T	I102N	0.981
17:5500655:G:T	A101D	0.980
17:5500632:A:G	C109R	0.976
17:5500684:A:C	F91L	0.976
17:5500684:A:T	F91L	0.976
17:5500686:A:G	F91L	0.976
17:5500666:G:C	F97L	0.975
17:5500666:G:T	F97L	0.975
17:5500668:A:G	F97L	0.975
17:5500640:A:T	I106N	0.974
17:5500645:G:C	F104L	0.974
17:5500645:G:T	F104L	0.974
17:5500647:A:G	F104L	0.974
17:5500624:A:C	F111L	0.972
17:5500624:A:T	F111L	0.972
17:5500626:A:G	F111L	0.972
17:5500656:C:G	A101P	0.968
17:5500610:A:G	L116S	0.967
17:5500635:A:G	S108P	0.967
17:5500646:A:G	F104S	0.963
17:5500658:G:T	A100E	0.963
17:5500640:A:C	I106S	0.962
17:5500640:A:G	I106T	0.962
17:5500644:A:G	S105P	0.961
17:5500676:A:T	L94H	0.954
17:5500628:A:T	I110N	0.952
17:5500634:G:T	S108Y	0.952
17:5500652:A:C	I102S	0.952
17:5500625:A:G	F111S	0.949

dbSNP variants (sampled 300 via entrez): RS1000278179 (17:5499144 G>C), RS1001287280 (17:5500177 C>A,T), RS1001579227 (17:5499828 G>T), RS1002180409 (17:5501048 G>A,C,T), RS1003302459 (17:5502591 G>A,T), RS1003599089 (17:5502383 A>G), RS1005315913 (17:5499544 A>G), RS1005430250 (17:5499786 C>A,G,T), RS1005903407 (17:5502116 T>C), RS1007318062 (17:5501953 T>G), RS1007431028 (17:5502336 C>A), RS1008004092 (17:5500014 C>A,T), RS1008925515 (17:5499224 A>G), RS1009933798 (17:5500426 T>C), RS1010181248 (17:5502773 T>A,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: 0 entries

Clinical trials (associated diseases)

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