C9orf57

Summary

C9orf57 (chromosome 9 open reading frame 57, HGNC:27037) is a protein-coding gene on chromosome 9q21.13, encoding Uncharacterized protein C9orf57 (Q5W0N0).

Predicted to be located in membrane.

Source: NCBI Gene 138240 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total — 1 pathogenic
• MANE Select transcript: NM_001128618

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27037
Approved symbol	C9orf57
Name	chromosome 9 open reading frame 57
Location	9q21.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204669
Ensembl biotype	protein_coding
Entrez	138240

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000377024, ENST00000424431, ENST00000651121, ENST00000651200, ENST00000652156, ENST00000652752, ENST00000673779

RefSeq mRNA: 2 — MANE Select: NM_001128618 NM_001128618, NM_001371610

CCDS: CCDS47980

Canonical transcript exons

ENST00000651200 — 5 exons

Exon	Start	End
ENSE00001472523	72056074	72056196
ENSE00001472527	72056784	72056843
ENSE00001876908	72051376	72052435
ENSE00003843056	72059235	72059384
ENSE00003848877	72060497	72060613

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 84.40.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0509 / max 41.0487, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100937	0.0189	3
100938	0.0165	3
100939	0.0155	3

Top tissues by expression

231 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	84.40	gold quality
right testis	UBERON:0004534	79.12	gold quality
left testis	UBERON:0004533	78.27	gold quality
testis	UBERON:0000473	76.89	gold quality
adult organism	UBERON:0007023	76.05	gold quality
ileal mucosa	UBERON:0000331	58.75	silver quality
pancreatic ductal cell	CL:0002079	55.40	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
deltoid	UBERON:0001476	52.36	gold quality
myocardium	UBERON:0002349	50.25	gold quality
quadriceps femoris	UBERON:0001377	47.18	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality
skin of hip	UBERON:0001554	43.68	silver quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
skeletal muscle tissue	UBERON:0001134	42.72	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
muscle tissue	UBERON:0002385	42.52	gold quality
sperm	CL:0000019	41.55	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
cartilage tissue	UBERON:0002418	40.77	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting C9orf57, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-185-5P	99.35	68.60	2497

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Uncharacterized protein C9orf57 — Q5W0N0 (reviewed: Q5W0N0)

All UniProt accessions (4): Q5W0N0, A0A494C027, A0A494C0F4, A0A494C1R2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5W0N0-1	1	yes
Q5W0N0-2	2

RefSeq proteins (2): NP_001122090, NP_001358539 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031710	DUF4723	Family

Pfam: PF15851

UniProt features (3 total): chain 1, transmembrane region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5W0N0-F1	69.04	0.20

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): chr9q21, ZNF274_TARGET_GENES, MIR4328, MIR4306, MIR1827, MIR3942_3P, MIR4446_5P, MIR6868_3P, MIR4723_5P, MIR6870_5P, MIR7111_5P, MIR5698, MIR6876_5P, MIR4476, MIR4649_3P

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

42 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C9orf57	C9orf85	Q96MD7	716
C9orf57	ABHD17B	Q5VST6	577
C9orf57	ZFAND5	O76080	507
C9orf57	CEMIP2	Q9UHN6	448
C9orf57	TRPM3	Q9HCF6	336
C9orf57	TMC2	Q8TDI7	287
C9orf57	TJP2	Q9UDY2	272
C9orf57	GJB2	P29033	271
C9orf57	TMC8	Q8IU68	264
C9orf57	ANXA1	P04083	222
C9orf57	SLC25A15	Q9Y619	213
C9orf57	MYO15A	Q9UKN7	203
C9orf57	ALDH1A1	P00352	202
C9orf57	OTOF	Q9HC10	192
C9orf57	CDH23	Q9H251	160

IntAct

1 interactions, top by confidence:

BioGRID (3): C9orf57 (Two-hybrid), GPSM3 (Two-hybrid), C9orf57 (Positive Genetic)

ESM2 similar proteins: A0A0J9YY54, A4K2M6, A4K2P0, A4K2P8, A4K2T3, A4K2U1, A4K2Y4, A6NF34, A6NI47, B3A0S1, D1FNK2, D3YZV8, D9IX97, O43493, P16225, P19957, P26436, P62521, Q06990, Q0P6D6, Q27J49, Q28139, Q29125, Q29126, Q4R729, Q4ZJY8, Q5F378, Q5JRC9, Q5QGU6, Q5SRN2, Q5W0N0, Q63HK3, Q6H9L7, Q6IC83, Q6S545, Q7M3V1, Q8BVC1, Q8CHN3, Q8N2N9, Q8N660

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
59107	GRCh38/hg38 9q21.13(chr9:72023067-72497412)x1	Pathogenic

SpliceAI

465 predictions. Top by Δscore:

Variant	Effect	Δscore
9:72056844:C:CC	acceptor_gain	0.9900
9:72060496:CCTAT:C	donor_gain	0.9900
9:72060500:T:C	donor_gain	0.9900
9:72056200:CAAG:C	acceptor_gain	0.9700
9:72056203:G:GC	acceptor_gain	0.9700
9:72056213:A:T	acceptor_gain	0.9700
9:72056856:CA:C	acceptor_gain	0.9700
9:72056203:G:C	acceptor_gain	0.9600
9:72056206:C:CT	acceptor_gain	0.9600
9:72056212:C:CT	acceptor_gain	0.9600
9:72056855:CCA:C	acceptor_gain	0.9600
9:72060492:CCTA:C	donor_loss	0.9600
9:72060493:CTAC:C	donor_loss	0.9600
9:72060494:TAC:T	donor_loss	0.9600
9:72060495:ACC:A	donor_loss	0.9600
9:72056844:CTAAA:C	acceptor_loss	0.9500
9:72056845:T:A	acceptor_loss	0.9500
9:72056857:A:C	acceptor_gain	0.9400
9:72059322:T:TA	donor_gain	0.9400
9:72052434:ACC:A	acceptor_loss	0.9300
9:72052435:CCT:C	acceptor_loss	0.9300
9:72052436:C:A	acceptor_loss	0.9300
9:72052437:T:A	acceptor_loss	0.9300
9:72056199:CCAAG:C	acceptor_gain	0.9300
9:72056207:A:T	acceptor_gain	0.9300
9:72056839:CAGGT:C	acceptor_gain	0.9300
9:72056853:A:T	acceptor_loss	0.9300
9:72056237:A:C	acceptor_gain	0.9200
9:72060490:GACCT:G	donor_loss	0.9200
9:72060491:ACCTA:A	donor_loss	0.9200

AlphaMissense

893 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:72052422:C:A	W120C	0.972
9:72052422:C:G	W120C	0.972
9:72056150:G:C	F90L	0.961
9:72056150:G:T	F90L	0.961
9:72056152:A:G	F90L	0.961
9:72052424:A:G	W120R	0.954
9:72052424:A:T	W120R	0.954
9:72056169:C:T	C84Y	0.930
9:72052405:C:G	C126S	0.929
9:72052406:A:T	C126S	0.929
9:72052380:G:C	F134L	0.925
9:72052380:G:T	F134L	0.925
9:72052382:A:G	F134L	0.925
9:72056178:C:G	C81S	0.919
9:72056179:A:T	C81S	0.919
9:72052384:C:G	C133S	0.917
9:72052385:A:T	C133S	0.917
9:72056179:A:G	C81R	0.917
9:72056177:G:C	C81W	0.916
9:72056178:C:T	C81Y	0.915
9:72056169:C:G	C84S	0.913
9:72056170:A:T	C84S	0.913
9:72056142:C:G	C93S	0.902
9:72056143:A:T	C93S	0.902
9:72052306:C:G	C159S	0.901
9:72052307:A:T	C159S	0.901
9:72052385:A:G	C133R	0.900
9:72056143:A:G	C93R	0.900
9:72056168:G:C	C84W	0.892
9:72052299:G:C	F161L	0.891

dbSNP variants (sampled 300 via entrez): RS1000108941 (9:72053397 A>G,T), RS1000292371 (9:72053703 C>T), RS1000555407 (9:72057868 A>G), RS1000652553 (9:72059482 T>C), RS1000897764 (9:72052071 A>G), RS1001003468 (9:72058177 T>A,C,G), RS1001201867 (9:72059572 A>G), RS1001221018 (9:72060872 T>C), RS1001320815 (9:72053504 C>T), RS1001437585 (9:72061640 C>A), RS1001517266 (9:72051708 A>G), RS1001563833 (9:72055129 G>A), RS1002422790 (9:72058420 C>G), RS1002891436 (9:72062245 T>C), RS1002994466 (9:72055135 C>T)

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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	decreases methylation	1
nonanal	decreases methylation	1
n-hexanal	decreases methylation	1
butyraldehyde	decreases methylation	1
caprylic aldehyde	decreases methylation	1
pentanal	decreases methylation	1
heptanal	decreases methylation	1

Clinical trials (associated diseases)

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