SMIM23

Summary

SMIM23 (small integral membrane protein 23, HGNC:34440) is a protein-coding gene on chromosome 5q35.1, encoding Small integral membrane protein 23 (A6NLE4).

Predicted to be located in plasma membrane.

Source: NCBI Gene 644994 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• MANE Select transcript: NM_001289970

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34440
Approved symbol	SMIM23
Name	small integral membrane protein 23
Location	5q35.1
Locus type	gene with protein product
Status	Approved
Aliases	LOC644994
Ensembl gene	ENSG00000185662
Ensembl biotype	protein_coding
Entrez	644994

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000523047, ENST00000639838, ENST00000640082

RefSeq mRNA: 1 — MANE Select: NM_001289970 NM_001289970

CCDS: CCDS87347

Canonical transcript exons

ENST00000523047 — 4 exons

Exon	Start	End
ENSE00000000287	171785817	171785976
ENSE00001305001	171790230	171790281
ENSE00001310729	171790482	171790549
ENSE00002129218	171790795	171791136

Expression profiles

Bgee: expression breadth broad, 64 present calls, max score 88.49.

Top tissues by expression

102 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	88.49	gold quality
left testis	UBERON:0004533	84.68	gold quality
testis	UBERON:0000473	83.95	gold quality
right testis	UBERON:0004534	83.54	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	64.65	gold quality
colonic epithelium	UBERON:0000397	59.45	gold quality
bone marrow cell	CL:0002092	55.71	gold quality
lower esophagus mucosa	UBERON:0035834	49.29	gold quality
skeletal muscle tissue	UBERON:0001134	47.46	silver quality
granulocyte	CL:0000094	46.95	silver quality
mucosa of stomach	UBERON:0001199	46.29	gold quality
sural nerve	UBERON:0015488	44.49	silver quality
bone marrow	UBERON:0002371	44.15	gold quality
tonsil	UBERON:0002372	43.97	gold quality
muscle tissue	UBERON:0002385	42.60	silver quality
body of pancreas	UBERON:0001150	41.14	silver quality
pancreas	UBERON:0001264	40.91	gold quality
spleen	UBERON:0002106	40.44	silver quality
duodenum	UBERON:0002114	40.04	gold quality
body of stomach	UBERON:0001161	39.94	gold quality
blood	UBERON:0000178	39.77	gold quality
gastrocnemius	UBERON:0001388	39.48	gold quality
islet of Langerhans	UBERON:0000006	39.38	gold quality
muscle of leg	UBERON:0001383	39.29	gold quality
stomach	UBERON:0000945	39.00	gold quality
metanephros cortex	UBERON:0010533	38.92	silver quality
ectocervix	UBERON:0012249	38.29	gold quality
cortex of kidney	UBERON:0001225	38.20	silver quality
thoracic aorta	UBERON:0001515	38.20	silver quality
ganglionic eminence	UBERON:0004023	38.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.92

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim23	ENSMUSG00000020270
rattus_norvegicus	Smim23	ENSRNOG00000027196

Protein

Protein identifiers

Small integral membrane protein 23 — A6NLE4 (reviewed: A6NLE4)

All UniProt accessions (1): A6NLE4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

RefSeq proteins (1): NP_001276899* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027880	DUF4635	Family

Pfam: PF15466

UniProt features (6 total): topological domain 2, chain 1, transmembrane region 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NLE4-F1	65.03	0.15

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, ZNF146_TARGET_GENES, GSE9037_CTRL_VS_LPS_1H_STIM_BMDM_DN, GSE8835_CD4_VS_CD8_TCELL_DN, GSE3039_NKT_CELL_VS_B1_BCELL_UP, chr5q35, GSE24210_IL35_TREATED_VS_UNTREATED_TCONV_CD4_TCELL_DN, GSE21063_CTRL_VS_ANTI_IGM_STIM_BCELL_NFATC1_KO_16H_UP, GSE41176_WT_VS_TAK1_KO_ANTI_IGM_STIM_BCELL_3H_UP, GSE41176_WT_VS_TAK1_KO_ANTI_IGM_STIM_BCELL_6H_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

132 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM23	DCHS2	Q6V1P9	646
SMIM23	COL17A1	Q9UMD9	577
SMIM23	CTBS	Q01459	536
SMIM23	PRDM16	Q9HAZ2	506
SMIM23	F8WDG0	F8WDG0	506
SMIM23	DHX35	Q9H5Z1	505
SMIM23	IQCJ-SCHIP1	B3KU38	505
SMIM23	PAX3	P23760	480
SMIM23	PDE8A	O60658	479
SMIM23	TENT4A	Q5XG87	468
SMIM23	MIPOL1	Q8TD10	448
SMIM23	PAX1	P15863	448
SMIM23	TP63	Q9H3D4	447
SMIM23	SHCBP1L	Q9BZQ2	425
SMIM23	TMCO5A	Q8N6Q1	419
SMIM23	SUPT3H	O75486	419

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTK4, A6NLE4, A8K554, F1MQW7, J3QMY9, O15273, O70548, O70552, P03246, P03247, P05857, P0DJZ2, P0DL12, P11305, P14254, P17758, P18097, P18801, P20919, P22378, P32543, P47939, P47940, P57738, Q0VD86, Q1X700, Q1X711, Q3TTJ4, Q5R7E2, Q5W5W9, Q61312, Q66669, Q66HF0, Q6GVM5, Q6UYE1, Q7L4S7, Q80VY2, Q86WR6, Q8K3A6, Q8N6T0

Diamond homologs: A6NLE4, Q9DAL0

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

402 predictions. Top by Δscore:

Variant	Effect	Δscore
5:171790972:G:GT	donor_gain	1.0000
5:171790894:G:GT	donor_gain	0.9900
5:171790957:G:GT	donor_gain	0.9900
5:171790959:A:T	donor_gain	0.9900
5:171790973:A:T	donor_gain	0.9900
5:171790975:G:GT	donor_gain	0.9900
5:171790997:G:GG	donor_gain	0.9900
5:171791007:G:GT	donor_gain	0.9900
5:171790334:TG:T	donor_gain	0.9800
5:171790335:GG:G	donor_gain	0.9800
5:171790360:T:G	donor_gain	0.9800
5:171790918:C:G	donor_gain	0.9800
5:171790945:G:GT	donor_gain	0.9800
5:171790974:G:GT	donor_gain	0.9800
5:171791007:G:T	donor_gain	0.9800
5:171785975:AGG:A	donor_loss	0.9700
5:171785977:G:A	donor_loss	0.9700
5:171785979:GAG:G	donor_loss	0.9700
5:171790353:T:TA	donor_gain	0.9700
5:171785973:GCAG:G	donor_gain	0.9600
5:171790991:A:G	donor_gain	0.9600
5:171791005:TGG:T	donor_gain	0.9600
5:171791006:GGG:G	donor_gain	0.9600
5:171794563:A:AG	acceptor_gain	0.9600
5:171794564:G:GG	acceptor_gain	0.9600
5:171790351:GGTT:G	donor_gain	0.9500
5:171790352:GTTG:G	donor_gain	0.9500
5:171790793:AG:A	acceptor_gain	0.9500
5:171790793:AGG:A	acceptor_gain	0.9500
5:171790794:GG:G	acceptor_gain	0.9500

AlphaMissense

1116 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:171790876:T:C	F103L	0.850
5:171790878:C:A	F103L	0.850
5:171790878:C:G	F103L	0.850
5:171790266:A:C	S48R	0.811
5:171790268:C:A	S48R	0.811
5:171790268:C:G	S48R	0.811
5:171790939:T:A	W124R	0.783
5:171790939:T:C	W124R	0.783
5:171790889:T:C	L107S	0.781
5:171790856:T:C	L96P	0.780
5:171790860:G:C	K97N	0.762
5:171790860:G:T	K97N	0.762
5:171790910:T:C	L114P	0.755
5:171790941:G:C	W124C	0.754
5:171790941:G:T	W124C	0.754
5:171790943:T:C	L125P	0.753
5:171790931:T:C	L121P	0.752
5:171790919:T:C	L117P	0.745
5:171790492:G:C	W56C	0.732
5:171790492:G:T	W56C	0.732
5:171790914:G:C	E115D	0.698
5:171790914:G:T	E115D	0.698
5:171790854:G:C	W95C	0.685
5:171790854:G:T	W95C	0.685
5:171790260:T:G	Y46D	0.658
5:171790868:T:C	L100S	0.652
5:171790877:T:C	F103S	0.647
5:171790852:T:A	W95R	0.642
5:171790852:T:C	W95R	0.642
5:171785973:G:C	K34N	0.625

dbSNP variants (sampled 300 via entrez): RS1000116045 (5:171771609 G>A), RS1000295985 (5:171772020 T>C), RS1000517749 (5:171774533 T>C), RS1000739236 (5:171779848 AAAG>A), RS1000795344 (5:171785673 T>C), RS1000905467 (5:171788375 A>C), RS1000934591 (5:171787935 A>G,T), RS1001111711 (5:171783056 G>C), RS1001170880 (5:171771744 C>T), RS1001254641 (5:171772916 C>G), RS1001290387 (5:171777400 G>A,C,T), RS1001395384 (5:171777230 C>G,T), RS1001581776 (5:171782467 G>A), RS1001635087 (5:171771936 G>A), RS1001673028 (5:171787508 C>A)

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

3 associations (top):

Study	Trait	p-value
GCST008839_137	Height	4.000000e-31
GCST008839_177	Height	3.000000e-25
GCST008839_462	Height	3.000000e-11

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
theaflavin-3,3’-digallate	affects expression	1
Acetaminophen	decreases expression	1

Clinical trials (associated diseases)

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