SMIM9

Summary

SMIM9 (small integral membrane protein 9, HGNC:41915) is a protein-coding gene on chromosome Xq28, encoding Small integral membrane protein 9 (A6NGZ8).

Predicted to be located in plasma membrane.

Source: NCBI Gene 100132963 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_001162936

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41915
Approved symbol	SMIM9
Name	small integral membrane protein 9
Location	Xq28
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203870
Ensembl biotype	protein_coding
Entrez	100132963

Gene structure

Transcript identifiers

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

ENST00000369529, ENST00000478043, ENST00000578244

RefSeq mRNA: 1 — MANE Select: NM_001162936 NM_001162936

CCDS: CCDS55546

Canonical transcript exons

ENST00000369529 — 5 exons

Exon	Start	End
ENSE00001450260	154823348	154823782
ENSE00001450263	154829535	154829664
ENSE00001450265	154830715	154830955
ENSE00001811986	154834563	154834662
ENSE00001867063	154832574	154832683

Expression profiles

Bgee: expression breadth ubiquitous, 105 present calls, max score 92.41.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
thymus	UBERON:0002370	92.41	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.13	gold quality
cerebellar vermis	UBERON:0004720	90.68	gold quality
quadriceps femoris	UBERON:0001377	90.00	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	63.23	gold quality
apex of heart	UBERON:0002098	62.10	gold quality
placenta	UBERON:0001987	59.62	gold quality
heart left ventricle	UBERON:0002084	53.62	gold quality
right lung	UBERON:0002167	51.72	gold quality
left testis	UBERON:0004533	48.13	gold quality
testis	UBERON:0000473	47.99	gold quality
right testis	UBERON:0004534	47.91	gold quality
heart	UBERON:0000948	47.74	gold quality
right atrium auricular region	UBERON:0006631	47.29	gold quality
gastrocnemius	UBERON:0001388	46.33	gold quality
spleen	UBERON:0002106	45.31	gold quality
omental fat pad	UBERON:0010414	45.07	gold quality
subcutaneous adipose tissue	UBERON:0002190	45.05	gold quality
adipose tissue	UBERON:0001013	44.77	gold quality
muscle of leg	UBERON:0001383	44.71	gold quality
metanephros cortex	UBERON:0010533	44.15	gold quality
left adrenal gland cortex	UBERON:0035825	42.91	gold quality
thoracic mammary gland	UBERON:0005200	41.50	gold quality
endocervix	UBERON:0000458	40.99	gold quality
bone marrow cell	CL:0002092	40.40	gold quality
lower esophagus muscularis layer	UBERON:0035833	39.64	gold quality
lower esophagus	UBERON:0013473	39.58	gold quality
adrenal tissue	UBERON:0018303	39.48	gold quality
liver	UBERON:0002107	38.85	gold quality
left adrenal gland	UBERON:0001234	38.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting SMIM9, 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-3688-3P	99.97	72.02	2834
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-2054	99.20	68.89	1699
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-3164	99.02	68.39	1071
HSA-MIR-6820-3P	99.02	68.50	1035
HSA-MIR-758-3P	98.42	68.60	1122
HSA-MIR-6792-5P	98.39	68.16	1330
HSA-MIR-6864-5P	98.38	66.59	1079
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-874-3P	95.02	65.66	806

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Smim9	ENSMUSG00000073094

Protein

Protein identifiers

Small integral membrane protein 9 — A6NGZ8 (reviewed: A6NGZ8)

All UniProt accessions (1): A6NGZ8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

RefSeq proteins (1): NP_001156408* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038853	Smim9	Family

UniProt features (5 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NGZ8-F1	68.19	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): chrXq28, ZNF768_TARGET_GENES, MIR23A_3P_MIR23B_3P, MIR23C, MIR9983_3P, MIR450B_5P, MIR129_5P, MIR605_3P, MIR6792_5P, MIR891B, MIR758_3P, MIR3164, MIR6820_3P, MIR6126, MIR6864_5P

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

52 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMIM9	TMEM210	A6NLX4	787
SMIM9	ZNF484	Q5JVG2	638
SMIM9	SMIM8	Q96KF7	626
SMIM9	SLC25A41	Q8N5S1	607
SMIM9	TOMM20L	Q6UXN7	582
SMIM9	CBY2	Q8NA61	528
SMIM9	RNF121	Q9H920	482
SMIM9	SLC25A2	Q9BXI2	474
SMIM9	PRRC2C	Q9Y520	468
SMIM9	RASEF	Q8IZ41	450
SMIM9	AAMP	Q13685	445
SMIM9	SMIM19	Q96E16	432
SMIM9	CTXND2	A0A1B0GV90	347
SMIM9	C1orf141	Q5JVX7	347
SMIM9	LDHAL6B	Q9BYZ2	324

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GSZ0, A2APA5, A2BDG0, A2BDG5, A2BDG9, A6NGZ8, C1J5M5, C1J5M7, P01286, P04640, P09916, P0CE40, P0DTF9, P16043, P40147, P40148, P54615, P56529, P58239, P58844, P80957, P86045, P86546, P86547, Q0H293, Q14CH0, Q16655, Q1JPW9, Q2KIK3, Q498C7, Q58CU5, Q5CZ51, Q5HZE8, Q5RD34, Q5VUB5, Q60549, Q6DJ00, Q6P995, Q6UWW9, Q7TNI2

Diamond homologs: A6NGZ8, Q3V0X1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

521 predictions. Top by Δscore:

Variant	Effect	Δscore
X:154829533:A:AC	donor_gain	1.0000
X:154829534:C:CC	donor_gain	1.0000
X:154830713:ACCC:A	donor_gain	1.0000
X:154830714:CCCC:C	donor_gain	1.0000
X:154830716:C:CA	donor_gain	1.0000
X:154830734:T:TA	donor_gain	1.0000
X:154830835:T:C	donor_gain	1.0000
X:154830862:C:CA	donor_gain	1.0000
X:154829528:AGCTT:A	donor_loss	0.9900
X:154829529:GCTT:G	donor_loss	0.9900
X:154829530:CTTAC:C	donor_loss	0.9900
X:154829531:TTA:T	donor_loss	0.9900
X:154829532:TACG:T	donor_loss	0.9900
X:154829533:A:AG	donor_loss	0.9900
X:154829534:C:G	donor_loss	0.9900
X:154830784:C:CT	donor_gain	0.9900
X:154830785:T:TT	donor_gain	0.9900
X:154830786:A:AC	donor_gain	0.9900
X:154830787:C:CC	donor_gain	0.9900
X:154830820:G:C	donor_gain	0.9900
X:154830841:G:C	donor_gain	0.9900
X:154830844:T:TA	donor_gain	0.9900
X:154832569:CTTA:C	donor_loss	0.9900
X:154832573:C:CA	donor_loss	0.9900
X:154823781:TG:T	acceptor_gain	0.9800
X:154823783:C:CC	acceptor_gain	0.9800
X:154829506:C:CA	donor_gain	0.9800
X:154830671:AAGT:A	donor_gain	0.9800
X:154832570:TTA:T	donor_gain	0.9800
X:154832571:TA:T	donor_gain	0.9800

AlphaMissense

623 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:154829554:C:G	G85R	0.878
X:154829554:C:T	G85R	0.878
X:154829542:A:G	C89R	0.847
X:154830829:C:G	G10R	0.787
X:154830829:C:T	G10R	0.787
X:154830817:A:G	C14R	0.776
X:154829553:C:T	G85E	0.749
X:154830828:C:T	G10E	0.749
X:154829580:G:T	A76D	0.747
X:154829562:G:T	A82E	0.739
X:154829576:A:C	F77L	0.712
X:154829576:A:T	F77L	0.712
X:154829578:A:G	F77L	0.712
X:154829545:A:G	C88R	0.710
X:154829589:G:T	A73D	0.682
X:154829559:A:C	L83R	0.647
X:154830805:A:G	C18R	0.629
X:154829571:A:C	L79R	0.625
X:154830824:A:C	F11L	0.625
X:154830824:A:T	F11L	0.625
X:154830826:A:G	F11L	0.625
X:154829547:A:T	L87H	0.608
X:154829540:G:C	C89W	0.605
X:154829571:A:T	L79H	0.600
X:154829648:C:A	W53C	0.600
X:154829648:C:G	W53C	0.600
X:154829574:A:C	L78R	0.599
X:154829547:A:C	L87R	0.576
X:154829636:G:C	F57L	0.570
X:154829636:G:T	F57L	0.570

dbSNP variants (sampled 300 via entrez): RS1000280469 (X:154834126 C>T), RS1000291086 (X:154823710 T>C), RS1000332234 (X:154833649 C>T), RS1000897747 (X:154826430 A>G), RS1001245323 (X:154826791 C>T), RS1001951974 (X:154831896 T>A), RS1004410035 (X:154830144 A>G), RS1004866293 (X:154829617 G>A), RS1006131262 (X:154827566 T>C), RS1006491632 (X:154827861 A>C), RS1006540587 (X:154833461 C>G), RS1007176418 (X:154822962 C>G), RS1007525384 (X:154835585 G>A), RS1007577548 (X:154835261 C>T), RS1008208934 (X:154831229 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

0 associations (top):

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
bisphenol A	decreases methylation	1
Benzo(a)pyrene	affects methylation, decreases methylation	1

Clinical trials (associated diseases)

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