SMIM42

Summary

SMIM42 (small integral membrane protein 42, HGNC:55000) is a protein-coding gene on chromosome 1q23.1, encoding Small integral membrane protein 42 (A0A5F9ZH02).

Predicted to be located in membrane.

Source: NCBI Gene 117981789 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001395415

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:55000
Approved symbol	SMIM42
Name	small integral membrane protein 42
Location	1q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000288460
Ensembl biotype	protein_coding
Entrez	117981789

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000672824

RefSeq mRNA: 1 — MANE Select: NM_001395415 NM_001395415

CCDS: CCDS91073

Canonical transcript exons

ENST00000672824 — 1 exons

Exon	Start	End
ENSE00003892534	158127287	158128301

Expression profiles

Bgee: expression breadth tissue_specific, 10 present calls, max score 89.37.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0077 / max 7.2174, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15295	0.0077	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.37	gold quality
right testis	UBERON:0004534	73.75	gold quality
left testis	UBERON:0004533	73.38	gold quality
testis	UBERON:0000473	72.82	gold quality
sural nerve	UBERON:0015488	48.44	gold quality
stromal cell of endometrium	CL:0002255	39.99	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
skeletal muscle tissue	UBERON:0001134	36.34	gold quality
mucosa of transverse colon	UBERON:0004991	36.25	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
calcaneal tendon	UBERON:0003701	33.31	gold quality
muscle tissue	UBERON:0002385	33.24	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
monocyte	CL:0000576	31.34	gold quality
leukocyte	CL:0000738	31.00	gold quality
endometrium	UBERON:0001295	30.50	gold quality
liver	UBERON:0002107	29.91	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
duodenum	UBERON:0002114	28.14	gold quality
urinary bladder	UBERON:0001255	27.95	gold quality
placenta	UBERON:0001987	27.72	gold quality
right coronary artery	UBERON:0001625	27.67	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	27.03	gold quality
islet of Langerhans	UBERON:0000006	26.96	gold quality

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Small integral membrane protein 42 — A0A5F9ZH02 (reviewed: A0A5F9ZH02)

All UniProt accessions (1): A0A5F9ZH02

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001382344* (*=MANE)

Domains & families (InterPro)

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A5F9ZH02-F1	71.43	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr1q23

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

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A5F9ZH02, A4IHD1, A4QJD5, A4QJL9, A6MVU6, B0YPP8, C0H3S8, G2TRL0, O78514, P03783, P0CA13, P11888, P18024, P19720, P22666, P26460, P29661, P35091, P38458, P39495, P43566, P46879, P48105, P50943, P51390, P86994, P89035, P92528, Q06FN9, Q06J12, Q12160, Q1CVG0, Q1XD97, Q2JLQ8, Q31652, Q3V0X1, Q4G381, Q5N554, Q61979, Q62649

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

449 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:158128048:G:C	F9L	0.967
1:158128048:G:T	F9L	0.967
1:158128050:A:G	F9L	0.967
1:158127956:A:T	V40D	0.966
1:158127965:A:C	M37R	0.964
1:158127938:A:T	V46D	0.950
1:158127965:A:T	M37K	0.947
1:158127947:A:C	L43R	0.936
1:158127950:A:C	L42R	0.932
1:158127950:A:G	L42P	0.927
1:158127936:A:G	W47R	0.926
1:158127936:A:T	W47R	0.926
1:158127947:A:T	L43H	0.924
1:158128042:C:A	W11C	0.924
1:158128042:C:G	W11C	0.924
1:158127986:A:T	L30H	0.923
1:158127959:A:C	L39R	0.922
1:158127974:G:T	T34K	0.921
1:158127986:A:C	L30R	0.919
1:158127974:G:C	T34R	0.914
1:158127989:A:T	V29D	0.913
1:158127947:A:G	L43P	0.909
1:158128044:A:G	W11R	0.897
1:158128044:A:T	W11R	0.897
1:158127968:A:C	L36R	0.891
1:158128016:A:T	I20K	0.881
1:158127941:A:G	L45P	0.875
1:158128049:A:G	F9S	0.871
1:158127922:T:A	K51N	0.868
1:158127922:T:G	K51N	0.868

dbSNP variants (sampled 300 via entrez): RS1000043936 (1:158129305 T>A), RS1000227927 (1:158127131 A>T), RS1002817253 (1:158128373 G>A,C), RS1003326617 (1:158127401 G>A,C), RS1003761872 (1:158129751 C>T), RS1004241449 (1:158129591 C>A,T), RS1004299020 (1:158128794 T>C), RS1004462508 (1:158127573 C>A,T), RS1006744319 (1:158129263 A>G), RS1006944398 (1:158128985 A>G), RS1008613388 (1:158127907 C>T), RS1008900707 (1:158129946 G>C), RS1009517500 (1:158129577 G>T), RS1010075291 (1:158126839 A>C), RS1010873841 (1:158129558 A>G)

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)

Clinical trials (associated diseases)

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