SMIM17

Summary

SMIM17 (small integral membrane protein 17, HGNC:27114) is a protein-coding gene on chromosome 19q13.43, encoding Small integral membrane protein 17 (P0DL12).

Predicted to be located in membrane.

Source: NCBI Gene 147670 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 21 total
• MANE Select transcript: NM_001193628

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27114
Approved symbol	SMIM17
Name	small integral membrane protein 17
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000268182
Ensembl biotype	protein_coding
Entrez	147670

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000598409, ENST00000600547

RefSeq mRNA: 1 — MANE Select: NM_001193628 NM_001193628

CCDS: CCDS58683

Canonical transcript exons

ENST00000598409 — 4 exons

Exon	Start	End
ENSE00003013452	56647558	56647634
ENSE00003050323	56655103	56657247
ENSE00003096529	56643159	56643210
ENSE00003126152	56645568	56645836

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 90.69.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9241 / max 100.4753, expressed in 95 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177732	0.8591	95
177731	0.0650	44

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 46	UBERON:0006483	90.69	gold quality
Brodmann (1909) area 23	UBERON:0013554	89.17	gold quality
superior vestibular nucleus	UBERON:0007227	88.41	gold quality
endothelial cell	CL:0000115	87.95	gold quality
middle temporal gyrus	UBERON:0002771	86.37	gold quality
hypothalamus	UBERON:0001898	84.14	gold quality
pons	UBERON:0000988	83.54	gold quality
buccal mucosa cell	CL:0002336	83.21	silver quality
superior frontal gyrus	UBERON:0002661	82.68	gold quality
prefrontal cortex	UBERON:0000451	81.78	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.76	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.68	gold quality
entorhinal cortex	UBERON:0002728	80.56	gold quality
postcentral gyrus	UBERON:0002581	80.48	gold quality
cerebral cortex	UBERON:0000956	80.22	gold quality
anterior cingulate cortex	UBERON:0009835	80.20	gold quality
frontal cortex	UBERON:0001870	79.91	gold quality
neocortex	UBERON:0001950	79.80	gold quality
primary visual cortex	UBERON:0002436	79.39	gold quality
Ammon’s horn	UBERON:0001954	79.11	gold quality
medulla oblongata	UBERON:0001896	78.92	gold quality
parietal lobe	UBERON:0001872	78.63	gold quality
substantia nigra pars compacta	UBERON:0001965	78.60	gold quality
cortical plate	UBERON:0005343	78.09	gold quality
cerebellar vermis	UBERON:0004720	77.70	silver quality
temporal lobe	UBERON:0001871	77.31	gold quality
occipital lobe	UBERON:0002021	76.70	gold quality
forebrain	UBERON:0001890	76.17	gold quality
brain	UBERON:0000955	75.94	gold quality
right frontal lobe	UBERON:0002810	75.74	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-10137	no	79.22
E-ANND-3	no	3.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

97 targeting SMIM17, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-1297	99.91	73.41	3162

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim17	ENSMUSG00000093536
rattus_norvegicus	Smim17	ENSRNOG00000067119

Protein

Protein identifiers

Small integral membrane protein 17 — P0DL12 (reviewed: P0DL12)

All UniProt accessions (2): P0DL12, M0R1N7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001180557* (*=MANE)

Domains & families (InterPro)

UniProt features (4 total): chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DL12-F1	59.88	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 51 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, PBXIP1_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR12136, MIR340_5P, MIR95_5P, MIR3133, MIR656_3P, MIR4311, MIR548AN, MIR29B_3P_MIR29C_3P, MIR29A_3P

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

186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM17	C3orf22	Q8N5N4	608
SMIM17	RNASE12	Q5GAN4	582
SMIM17	C12orf56	Q8IXR9	577
SMIM17	TMEM214	Q6NUQ4	576
SMIM17	TMEM68	Q96MH6	558
SMIM17	SH2D7	A6NKC9	543
SMIM17	CC2D2B	Q6DHV5	541
SMIM17	C22orf42	Q6IC83	540
SMIM17	C1orf167	Q5SNV9	540
SMIM17	AMZ2	Q86W34	527
SMIM17	ANKRD62	A6NC57	527
SMIM17	CLPSL1	A2RUU4	515
SMIM17	SPDYE4	A6NLX3	507
SMIM17	EPCIP	Q9NYP8	507
SMIM17	RD3L	P0DJH9	507

IntAct

0 interactions, top by confidence:

BioGRID (3): TPM4 (Cross-Linking-MS (XL-MS)), SMIM17 (Affinity Capture-MS), SMIM17 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8I316, A0A1W2PR82, A0A286YDK6, A5PJD3, A6H7B4, A6NEV1, A6NGY1, A6NHS1, A6QP24, A8MUA0, A8MUI8, A8MV72, A8MX80, A8MYA2, D3ZAQ5, O60393, P0C1T1, P0DL12, P43359, Q0KK55, Q0VD86, Q1RN00, Q32LI3, Q3UN58, Q3ZCQ2, Q5M831, Q5M844, Q66H53, Q68US1, Q6AYA8, Q6DIA7, Q6K1E7, Q6PE65, Q6ZW13, Q80VY2, Q8BII1, Q8IY42, Q8N9G6, Q8NA77, Q8TDR4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

846 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56643209:GG:G	donor_gain	1.0000
19:56643210:GG:G	donor_gain	1.0000
19:56643206:GGAGG:G	donor_gain	0.9900
19:56643207:GAGG:G	donor_gain	0.9900
19:56643207:GAGGG:G	donor_gain	0.9900
19:56643211:G:GG	donor_gain	0.9900
19:56643212:T:TC	donor_loss	0.9900
19:56643213:G:GT	donor_loss	0.9900
19:56645566:AGTCC:A	acceptor_loss	0.9900
19:56645832:GAAAG:G	donor_gain	0.9900
19:56645833:AAAG:A	donor_loss	0.9900
19:56645834:AAG:A	donor_loss	0.9900
19:56645837:GT:G	donor_loss	0.9900
19:56645838:T:G	donor_loss	0.9900
19:56643214:AGT:A	donor_loss	0.9800
19:56645567:G:GT	acceptor_gain	0.9800
19:56645592:T:TA	acceptor_gain	0.9800
19:56647540:A:AG	acceptor_gain	0.9800
19:56647546:A:AG	acceptor_gain	0.9800
19:56647547:C:G	acceptor_gain	0.9800
19:56643215:G:C	donor_loss	0.9700
19:56645566:A:AG	acceptor_gain	0.9700
19:56645567:GT:G	acceptor_gain	0.9700
19:56645594:G:C	acceptor_gain	0.9700
19:56645567:GTCCT:G	acceptor_gain	0.9600
19:56647552:A:AG	acceptor_gain	0.9600
19:56647541:C:G	acceptor_gain	0.9500
19:56655096:GTTTC:G	acceptor_loss	0.9500
19:56655097:TTTCA:T	acceptor_loss	0.9500
19:56655098:TTCA:T	acceptor_loss	0.9500

AlphaMissense

769 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:56655157:T:C	C101R	0.988
19:56655179:T:A	V108D	0.965
19:56655166:T:C	F104L	0.960
19:56655168:T:A	F104L	0.960
19:56655168:T:G	F104L	0.960
19:56655146:T:A	V97D	0.957
19:56655188:G:A	G111E	0.950
19:56655172:T:C	F106L	0.946
19:56655174:C:A	F106L	0.946
19:56655174:C:G	F106L	0.946
19:56655176:T:C	L107P	0.944
19:56655161:T:A	V102E	0.942
19:56655187:G:A	G111R	0.942
19:56655187:G:C	G111R	0.942
19:56655176:T:G	L107R	0.938
19:56655182:T:C	L109S	0.935
19:56655187:G:T	G111W	0.926
19:56655185:C:A	T110K	0.923
19:56655194:C:A	P113H	0.923
19:56655164:T:G	L103R	0.921
19:56655152:T:A	V99E	0.920
19:56655167:T:C	F104S	0.914
19:56655164:T:A	L103H	0.913
19:56655173:T:C	F106S	0.911
19:56655143:T:A	I96K	0.908
19:56655194:C:G	P113R	0.905
19:56655176:T:A	L107Q	0.903
19:56655158:G:A	C101Y	0.892
19:56655159:C:G	C101W	0.891
19:56655170:T:C	L105S	0.891

dbSNP variants (sampled 300 via entrez): RS1000133054 (19:56654257 G>A), RS1000262626 (19:56649617 G>C), RS1000312546 (19:56651883 C>T), RS1000395072 (19:56645888 G>A,T), RS1000593495 (19:56649318 A>G), RS1001128526 (19:56653118 C>A,G), RS1001645068 (19:56644433 T>C), RS1001656050 (19:56654899 A>T), RS1001756505 (19:56651127 G>A), RS1001947306 (19:56650230 T>C), RS1002212057 (19:56653675 C>A), RS1002320351 (19:56656316 A>G,T), RS1002359404 (19:56641587 T>C), RS1002367562 (19:56653850 T>A), RS1002951530 (19:56656417 T>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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Valproic Acid	increases expression	1

Clinical trials (associated diseases)

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