SMIM19

Summary

SMIM19 (small integral membrane protein 19, HGNC:25166) is a protein-coding gene on chromosome 8p11.21, encoding Small integral membrane protein 19 (Q96E16).

Predicted to be located in membrane.

Source: NCBI Gene 114926 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 25 total
• MANE Select transcript: NM_001135674

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25166
Approved symbol	SMIM19
Name	small integral membrane protein 19
Location	8p11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000176209
Ensembl biotype	protein_coding
Entrez	114926

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 18 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000414154, ENST00000416469, ENST00000417410, ENST00000438528, ENST00000490331, ENST00000498447, ENST00000518574, ENST00000529505, ENST00000908389, ENST00000908390, ENST00000908391, ENST00000908392, ENST00000908393, ENST00000908394, ENST00000908395, ENST00000908396, ENST00000908397, ENST00000926900, ENST00000926901, ENST00000966126

RefSeq mRNA: 5 — MANE Select: NM_001135674 NM_001135674, NM_001135675, NM_001135676, NM_001363186, NM_138436

CCDS: CCDS6133

Canonical transcript exons

ENST00000417410 — 4 exons

Exon	Start	End
ENSE00001660557	42541585	42542373
ENSE00003572162	42548656	42548780
ENSE00003613896	42546469	42546606
ENSE00003901524	42552544	42555195

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 98.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.6761 / max 271.7269, expressed in 1819 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
88691	32.1870	1819
88692	2.1308	1235
88690	1.7714	1107
205172	0.1765	58
205171	0.1489	46
88694	0.1370	42
88695	0.0727	17
88693	0.0518	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	98.94	gold quality
left ventricle myocardium	UBERON:0006566	98.27	gold quality
bronchial epithelial cell	CL:0002328	98.24	gold quality
kidney epithelium	UBERON:0004819	98.20	gold quality
tibialis anterior	UBERON:0001385	98.14	gold quality
bronchus	UBERON:0002185	97.95	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.70	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.64	gold quality
upper arm skin	UBERON:0004263	97.56	gold quality
deltoid	UBERON:0001476	97.54	gold quality
nasal cavity mucosa	UBERON:0001826	97.51	gold quality
vastus lateralis	UBERON:0001379	97.49	gold quality
myocardium	UBERON:0002349	97.34	gold quality
biceps brachii	UBERON:0001507	97.28	gold quality
ileal mucosa	UBERON:0000331	97.07	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.88	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.86	gold quality
tendon of biceps brachii	UBERON:0008188	96.86	gold quality
skeletal muscle tissue	UBERON:0001134	96.84	gold quality
quadriceps femoris	UBERON:0001377	96.64	gold quality
body of pancreas	UBERON:0001150	96.52	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.46	gold quality
nasal cavity epithelium	UBERON:0005384	96.28	gold quality
tendon	UBERON:0000043	96.26	gold quality
right uterine tube	UBERON:0001302	96.13	gold quality
calcaneal tendon	UBERON:0003701	96.13	gold quality
muscle tissue	UBERON:0002385	96.11	gold quality
upper leg skin	UBERON:0004262	96.07	gold quality
skin of hip	UBERON:0001554	96.06	gold quality
corpus epididymis	UBERON:0004359	95.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting SMIM19, 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-4795-3P	100.00	74.62	4024
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-1324	99.46	66.57	1302
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-1273H-3P	99.29	67.55	980
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-1304-3P	98.29	66.44	1207
HSA-MIR-3166	98.24	66.63	1223
HSA-MIR-432-5P	98.00	68.13	989
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-6807-5P	97.51	64.25	1046

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	smim19	ENSDARG00000037423
mus_musculus	Smim19	ENSMUSG00000031534
rattus_norvegicus	Smim19	ENSRNOG00000024930

Protein

Protein identifiers

Small integral membrane protein 19 — Q96E16 (reviewed: Q96E16)

All UniProt accessions (3): E5RII4, E5RKA7, Q96E16

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the SMIM19 family.

RefSeq proteins (5): NP_001129146, NP_001129147, NP_001129148, NP_001350115, NP_612445 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029368	SMIM19	Family

Pfam: PF15117

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96E16-F1	68.02	0.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): E4F1_Q6, RYTTCCTG_ETS2_B, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, MARTENS_TRETINOIN_RESPONSE_DN, PEDRIOLI_MIR31_TARGETS_DN, GSE13522_WT_VS_IFNAR_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN, PCGF1_TARGET_GENES, SUPT16H_TARGET_GENES, ZNF618_TARGET_GENES, MIR7154_5P, MIR589_3P, MIR2110, MIR433_3P, GSE11864_CSF1_VS_CSF1_IFNG_PAM3CYS_IN_MAC_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

234 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM19	OR8B12	Q8NGG6	571
SMIM19	OR8B3	Q8NGG8	528
SMIM19	ZNF484	Q5JVG2	514
SMIM19	A0A2U3TZT1	A0A2U3TZT1	506
SMIM19	ANKMY2	Q8IV38	448
SMIM19	TBATA	Q96M53	435
SMIM19	SMIM9	A6NGZ8	432
SMIM19	TBC1D8B	Q0IIM8	431
SMIM19	SETD9	Q8NE22	420
SMIM19	C10orf90	Q96M02	400
SMIM19	NXNL1	Q96CM4	386
SMIM19	EME2	A4GXA9	379
SMIM19	DENND5B	Q6ZUT9	377
SMIM19	CPNE8	Q86YQ8	370
SMIM19	KIF12	Q96FN5	366
SMIM19	SLC20A2	Q08357	366

IntAct

16 interactions, top by confidence:

A	B	Type	Score
UBQLN2	SMIM19	psi-mi:“MI:0915”(physical association)	0.560
UBQLN1	SMIM19	psi-mi:“MI:0915”(physical association)	0.560
GET3	SMIM19	psi-mi:“MI:0915”(physical association)	0.560
ASPH	SMIM19	psi-mi:“MI:0915”(physical association)	0.560
JAGN1	SMIM19	psi-mi:“MI:0915”(physical association)	0.560
SMIM19	UBQLN2	psi-mi:“MI:0915”(physical association)	0.560
SMIM19	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
JAGN1	SMIM19	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): SMIM19 (Two-hybrid), SMIM19 (Two-hybrid), UBQLN2 (Two-hybrid), ASNA1 (Two-hybrid), ASPH (Two-hybrid), SMIM19 (Proximity Label-MS), SMIM19 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GQX3, A0A1B0GRQ0, A0A1B0GV90, A4D0T7, A4QNL6, A6NFZ4, A9RA88, B0CMA4, B3DHH5, C0HJJ0, C1PGW0, D3YUK8, F2Z3Y9, F5HFG3, G1TZA0, G2TRP0, O13001, O14068, O39920, P0DKX4, P34535, P57054, P61807, P61808, Q06FW7, Q19443, Q3E8L0, Q3E912, Q3T0S0, Q4V921, Q54L98, Q5F3W2, Q5R687, Q5RBD8, Q5U4Q2, Q66J27, Q6PQZ3, Q80UA9, Q80ZU4, Q8AUU1

Diamond homologs: A4QNL6, A5D7B5, Q4V921, Q5RBD8, Q80ZU4, Q96E16

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

799 predictions. Top by Δscore:

Variant	Effect	Δscore
8:42541222:T:TA	donor_gain	1.0000
8:42548777:ATTT:A	donor_gain	1.0000
8:42548778:TTT:T	donor_gain	1.0000
8:42548781:G:GG	donor_gain	1.0000
8:42552532:T:A	acceptor_gain	1.0000
8:42552535:T:A	acceptor_gain	1.0000
8:42552537:T:TA	acceptor_gain	1.0000
8:42552542:A:AG	acceptor_gain	1.0000
8:42552543:G:GG	acceptor_gain	1.0000
8:42552630:G:GT	donor_gain	1.0000
8:42541824:C:A	donor_gain	0.9900
8:42546467:A:AG	acceptor_gain	0.9900
8:42546468:G:GA	acceptor_gain	0.9900
8:42546468:GC:G	acceptor_gain	0.9900
8:42546468:GCC:G	acceptor_gain	0.9900
8:42546468:GCCCC:G	acceptor_gain	0.9900
8:42546602:AAAAG:A	donor_loss	0.9900
8:42546603:AAAG:A	donor_loss	0.9900
8:42546604:AAG:A	donor_loss	0.9900
8:42546605:AG:A	donor_loss	0.9900
8:42546606:GGT:G	donor_loss	0.9900
8:42546607:G:A	donor_loss	0.9900
8:42546608:T:G	donor_loss	0.9900
8:42548639:ATG:A	acceptor_gain	0.9900
8:42548776:CATTT:C	donor_gain	0.9900
8:42548779:TTGT:T	donor_loss	0.9900
8:42548780:TG:T	donor_loss	0.9900
8:42548781:G:GC	donor_loss	0.9900
8:42548782:TAAGT:T	donor_loss	0.9900
8:42548783:A:AT	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000266422 (8:42547336 G>A,C), RS1000973972 (8:42541276 G>A), RS1001026264 (8:42541568 G>A), RS1001058815 (8:42551084 C>T), RS1001286437 (8:42543835 A>G), RS1001316196 (8:42546709 A>G), RS1001402389 (8:42543451 G>T), RS1001584198 (8:42550226 C>T), RS1002469777 (8:42540691 T>C), RS1002700846 (8:42545392 G>A), RS1003078896 (8:42552217 A>C), RS1003313941 (8:42543578 A>G), RS1003415000 (8:42550537 C>T), RS1003747467 (8:42542253 C>A,T), RS1003849503 (8:42542124 G>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:213600, MIM:606656

GenCC curated gene-disease

Mondo (1): basal ganglia calcification, idiopathic, 1 (MONDO:0024538)

Orphanet (1): Bilateral striopallidodentate calcinosis (Orphanet:1980)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST003854_24	Gut microbiota (functional units)	4.000000e-08
GCST004329_1	Mean corpuscular hemoglobin concentration	5.000000e-07
GCST004329_2	Mean corpuscular hemoglobin concentration	3.000000e-11
GCST010083_246	Hemoglobin levels	8.000000e-26
GCST010703_179	Brain morphology (MOSTest)	5.000000e-11
GCST90000047_154	Age at first sexual intercourse	1.000000e-10
GCST90002384_175	Hemoglobin	1.000000e-33

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007874	gut microbiome measurement
EFO:0004528	mean corpuscular hemoglobin concentration
EFO:0004509	hemoglobin measurement
EFO:0004346	neuroimaging measurement
EFO:0009749	age at first sexual intercourse measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537657	Basal ganglia calcification, idiopathic 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	4
GSK-J4	decreases expression	1
resorcinol	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
pyrachlostrobin	decreases expression	1
picoxystrobin	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	increases expression	1
Estradiol	decreases expression	1
Formaldehyde	increases expression	1
Hydrogen Peroxide	affects expression	1
Ketoconazole	decreases expression	1
Quercetin	decreases expression	1
Smoke	increases expression	1
Tretinoin	decreases expression	1
Tunicamycin	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
tert-Butylhydroperoxide	affects expression	1
Vitamin K 3	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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