C9orf50

Summary

C9orf50 (chromosome 9 open reading frame 50, HGNC:23677) is a protein-coding gene on chromosome 9q34.11, encoding Uncharacterized protein C9orf50 (Q5SZB4).

Located in cytoplasm.

Source: NCBI Gene 375759 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 10 total — 1 pathogenic
• MANE Select transcript: NM_199350

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23677
Approved symbol	C9orf50
Name	chromosome 9 open reading frame 50
Location	9q34.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35803
Ensembl gene	ENSG00000179058
Ensembl biotype	protein_coding
Entrez	375759

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000372478, ENST00000619117, ENST00000651030

RefSeq mRNA: 1 — MANE Select: NM_199350 NM_199350

CCDS: CCDS35159

Canonical transcript exons

ENST00000372478 — 7 exons

Exon	Start	End
ENSE00001236502	129613435	129613597
ENSE00001236506	129615484	129615647
ENSE00001236510	129619520	129619636
ENSE00001236515	129619740	129619830
ENSE00001236524	129613107	129613251
ENSE00001457906	129612225	129612454
ENSE00003978305	129620067	129621101

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 75.57.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	75.57	gold quality
left ventricle myocardium	UBERON:0006566	75.49	gold quality
tendon of biceps brachii	UBERON:0008188	74.17	gold quality
left testis	UBERON:0004533	70.95	gold quality
right testis	UBERON:0004534	70.30	gold quality
buccal mucosa cell	CL:0002336	69.80	silver quality
myocardium	UBERON:0002349	69.70	gold quality
kidney epithelium	UBERON:0004819	68.50	gold quality
sperm	CL:0000019	68.49	gold quality
testis	UBERON:0000473	68.29	gold quality
nasal cavity epithelium	UBERON:0005384	67.22	gold quality
quadriceps femoris	UBERON:0001377	65.16	gold quality
vastus lateralis	UBERON:0001379	64.85	gold quality
upper arm skin	UBERON:0004263	63.84	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	63.49	gold quality
medial globus pallidus	UBERON:0002477	63.44	gold quality
tibialis anterior	UBERON:0001385	63.13	silver quality
cartilage tissue	UBERON:0002418	62.28	gold quality
tibial nerve	UBERON:0001323	61.77	gold quality
stromal cell of endometrium	CL:0002255	61.72	gold quality
biceps brachii	UBERON:0001507	61.69	gold quality
tibia	UBERON:0000979	61.50	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	61.35	gold quality
pancreatic ductal cell	CL:0002079	61.06	silver quality
deltoid	UBERON:0001476	60.21	gold quality
globus pallidus	UBERON:0001875	60.06	gold quality
vena cava	UBERON:0004087	59.91	gold quality
parotid gland	UBERON:0001831	59.61	gold quality
secondary oocyte	CL:0000655	59.52	gold quality
hypothalamus	UBERON:0001898	59.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting C9orf50, 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-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-3176	99.25	64.35	954
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-4317	98.49	67.09	987
HSA-MIR-550B-2-5P	96.56	64.61	646
HSA-MIR-6796-5P	95.37	66.08	1120

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700001O22Rik	ENSMUSG00000044320
rattus_norvegicus	C3h9orf50	ENSRNOG00000018486

Protein

Protein identifiers

Uncharacterized protein C9orf50 — Q5SZB4 (reviewed: Q5SZB4)

All UniProt accessions (2): Q5SZB4, A0A087WX76

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

RefSeq proteins (1): NP_955382* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032756	DUF4685	Domain

Pfam: PF15737

UniProt features (12 total): sequence variant 4, compositionally biased region 3, region of interest 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SZB4-F1	44.79	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, chr9q34, ZNF664_TARGET_GENES, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP, GSE10239_MEMORY_VS_KLRG1HIGH_EFF_CD8_TCELL_UP, MIR6796_5P, MIR3151_5P, GSE15750_DAY6_VS_DAY10_TRAF6KO_EFF_CD8_TCELL_DN, GSE17721_CTRL_VS_PAM3CSK4_1H_BMDC_DN, GSE17721_CTRL_VS_CPG_2H_BMDC_DN, GSE20366_CD103_POS_VS_CD103_KLRG1_DP_TREG_DN, GSE39820_TGFBETA1_VS_TGFBETA3_IN_IL6_IL23A_TREATED_CD4_TCELL_DN, GSE37534_GW1929_VS_ROSIGLITAZONE_TREATED_CD4_TCELL_PPARG1_FOXP3_TRANSDUCED_UP, GSE43863_DAY6_EFF_VS_DAY150_MEM_TFH_CD4_TCELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

252 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C9orf50	KCNQ5	Q9NR82	579
C9orf50	CLIP4	Q8N3C7	571
C9orf50	NDRG4	Q9ULP0	516
C9orf50	C3orf22	Q8N5N4	480
C9orf50	SEPTIN9	Q9UHD8	475
C9orf50	RNASE12	Q5GAN4	444
C9orf50	C12orf56	Q8IXR9	435
C9orf50	SMIM17	P0DL12	419
C9orf50	AMER2	Q8N7J2	418
C9orf50	SH2D7	A6NKC9	407
C9orf50	C1orf167	Q5SNV9	400
C9orf50	CC2D2B	Q6DHV5	400
C9orf50	C22orf42	Q6IC83	399
C9orf50	ANKRD62	A6NC57	398
C9orf50	SPDYE4	A6NLX3	392

IntAct

3 interactions, top by confidence:

A	B	Type	Score
PPP1CC	C9orf50	psi-mi:“MI:0915”(physical association)	0.370
C9orf50	PPP1CC	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (3): C9orf50 (Positive Genetic), C9orf50 (Positive Genetic), C9orf50 (Two-hybrid)

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A2VE02, A5D7I0, A6NDY2, A6NGG8, A6NIJ5, A6NNJ1, A8MXJ8, A8MYA2, B1ASB6, B2RW88, D6RGX4, O60269, P0C7V4, P0C7W8, P0C7W9, P0C7X0, P0DV75, P0DV76, Q2KIS6, Q2NL68, Q3SY00, Q4R736, Q4V8B5, Q5RCQ2, Q5SZB4, Q5VZ46, Q5XIK6, Q658T7, Q66JV7, Q6NS69, Q6PAC4, Q6ZMY3, Q76N32, Q7TSA6, Q7Z591, Q80VW7, Q80X53

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	1
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1527562	GRCh37/hg19 9q34.11(chr9:130390139-132760275)	Pathogenic

SpliceAI

1468 predictions. Top by Δscore:

Variant	Effect	Δscore
9:129613420:T:TA	donor_gain	1.0000
9:129613477:T:TA	donor_gain	1.0000
9:129613513:T:A	donor_gain	1.0000
9:129613598:C:CC	acceptor_gain	1.0000
9:129620065:A:AC	donor_gain	1.0000
9:129620066:C:CC	donor_gain	1.0000
9:129613251:CCT:C	acceptor_loss	0.9900
9:129613333:CA:C	donor_gain	0.9900
9:129613421:C:A	donor_gain	0.9900
9:129613433:A:AC	donor_gain	0.9900
9:129613433:ACAGG:A	donor_gain	0.9900
9:129613434:C:CC	donor_gain	0.9900
9:129613434:CAGG:C	donor_gain	0.9900
9:129613434:CAGGC:C	donor_gain	0.9900
9:129613494:CAGGG:C	donor_gain	0.9900
9:129613533:C:CA	donor_gain	0.9900
9:129613594:TGGA:T	acceptor_gain	0.9900
9:129613595:GGA:G	acceptor_gain	0.9900
9:129613596:GA:G	acceptor_gain	0.9900
9:129613596:GACTG:G	acceptor_loss	0.9900
9:129613598:C:T	acceptor_loss	0.9900
9:129619518:A:AC	donor_gain	0.9900
9:129619519:C:CC	donor_gain	0.9900
9:129620066:CT:C	donor_gain	0.9900
9:129620069:A:AC	donor_gain	0.9900
9:129613252:C:CC	acceptor_gain	0.9800
9:129613414:T:TA	donor_gain	0.9800
9:129613593:TTGGA:T	acceptor_gain	0.9800
9:129614979:AGCTT:A	donor_gain	0.9800
9:129614980:G:C	donor_gain	0.9800

AlphaMissense

2720 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:129620113:G:C	F154L	0.964
9:129620113:G:T	F154L	0.964
9:129620115:A:G	F154L	0.964
9:129615539:G:C	F275L	0.962
9:129615539:G:T	F275L	0.962
9:129615541:A:G	F275L	0.962
9:129620122:G:C	F151L	0.936
9:129620122:G:T	F151L	0.936
9:129620124:A:G	F151L	0.936
9:129615551:G:C	F271L	0.919
9:129615551:G:T	F271L	0.919
9:129615553:A:G	F271L	0.919
9:129620114:A:G	F154S	0.899
9:129615500:C:A	W288C	0.896
9:129615500:C:G	W288C	0.896
9:129615531:T:A	E278V	0.894
9:129615520:C:G	D282H	0.879
9:129619754:G:C	F195L	0.878
9:129619754:G:T	F195L	0.878
9:129619756:A:G	F195L	0.878
9:129615540:A:G	F275S	0.877
9:129615498:T:A	E289V	0.866
9:129615540:A:C	F275C	0.863
9:129615518:G:C	D282E	0.855
9:129615518:G:T	D282E	0.855
9:129613134:G:C	F387L	0.847
9:129613134:G:T	F387L	0.847
9:129613136:A:G	F387L	0.847
9:129615508:G:T	R286S	0.847
9:129619543:G:C	F231L	0.842

dbSNP variants (sampled 300 via entrez): RS1000319099 (9:129619251 A>G,T), RS1000859678 (9:129621294 C>G), RS1000889691 (9:129614956 A>G), RS1001261290 (9:129615195 G>A,T), RS1001322600 (9:129620438 G>A,C), RS1001325390 (9:129615403 T>A,C), RS1001805189 (9:129620288 A>G), RS1001853025 (9:129616115 C>T), RS1002292850 (9:129620512 G>A,C), RS1002407492 (9:129620868 G>A), RS1002623621 (9:129619173 G>A), RS1002753033 (9:129613863 G>A,C), RS1002829526 (9:129615157 G>A,C), RS1002889054 (9:129617238 G>A), RS1003047125 (9:129612021 A>G)

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

2 associations (top):

Study	Trait	p-value
GCST001308_16	Response to anti-depressant treatment in major depressive disorder	3.000000e-06
GCST002118_9	Metabolite levels (Pyroglutamine)	8.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006321	antidepressant-induced dizziness
EFO:0005408	pyroglutamine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol F	affects cotreatment, increases methylation	1
sodium arsenite	increases expression	1
tebuconazole	decreases expression	1
MRK 003	decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Endosulfan	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Antirheumatic Agents	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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