C17orf50

Summary

C17orf50 (chromosome 17 open reading frame 50, HGNC:29581) is a protein-coding gene on chromosome 17q12, encoding Uncharacterized protein C17orf50 (Q8WW18).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 13 total — 1 pathogenic
• MANE Select transcript: NM_145272

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29581
Approved symbol	C17orf50
Name	chromosome 17 open reading frame 50
Location	17q12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000270806
Ensembl biotype	protein_coding
Entrez	146853

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000603305, ENST00000604830, ENST00000605587

RefSeq mRNA: 1 — MANE Select: NM_145272 NM_145272

CCDS: CCDS42298

Canonical transcript exons

ENST00000605587 — 3 exons

Exon	Start	End
ENSE00003462919	35760887	35760954
ENSE00003525875	35764426	35765079
ENSE00003602126	35764007	35764325

Expression profiles

Bgee: expression breadth ubiquitous, 118 present calls, max score 95.14.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1705 / max 174.5699, expressed in 4 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160378	0.1520	4
160377	0.0106	3
160376	0.0042	2
160379	0.0036	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	95.14	gold quality
right testis	UBERON:0004534	94.96	gold quality
sperm	CL:0000019	92.80	gold quality
testis	UBERON:0000473	91.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.54	silver quality
adult organism	UBERON:0007023	80.89	gold quality
kidney epithelium	UBERON:0004819	63.63	gold quality
sural nerve	UBERON:0015488	62.03	gold quality
biceps brachii	UBERON:0001507	61.03	gold quality
deltoid	UBERON:0001476	60.32	gold quality
right uterine tube	UBERON:0001302	60.27	gold quality
tibialis anterior	UBERON:0001385	60.13	silver quality
nasal cavity epithelium	UBERON:0005384	59.07	gold quality
corpus epididymis	UBERON:0004359	58.84	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	58.65	gold quality
cauda epididymis	UBERON:0004360	58.46	gold quality
bronchial epithelial cell	CL:0002328	56.69	gold quality
myocardium	UBERON:0002349	56.60	gold quality
mucosa of paranasal sinus	UBERON:0005030	56.50	gold quality
nucleus accumbens	UBERON:0001882	56.06	gold quality
bronchus	UBERON:0002185	55.94	gold quality
nasal cavity mucosa	UBERON:0001826	55.51	gold quality
gingival epithelium	UBERON:0001949	55.38	gold quality
caput epididymis	UBERON:0004358	55.20	gold quality
cartilage tissue	UBERON:0002418	55.09	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.98	gold quality
gingiva	UBERON:0001828	54.38	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
jejunal mucosa	UBERON:0000399	54.20	gold quality
ileal mucosa	UBERON:0000331	54.15	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting C17orf50, 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-29B-2-5P	99.67	68.98	1726
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-4257	97.86	68.05	1190
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-12128	96.67	66.98	1471
HSA-MIR-4790-3P	96.63	67.08	806
HSA-MIR-1237-5P	95.38	62.21	451
HSA-MIR-4488	95.38	62.00	443
HSA-MIR-4697-5P	95.38	61.72	457

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700020L24Rik	ENSMUSG00000035085
rattus_norvegicus	C10h17orf50	ENSRNOG00000049757

Protein

Protein identifiers

Uncharacterized protein C17orf50 — Q8WW18 (reviewed: Q8WW18)

All UniProt accessions (3): Q8WW18, A0A075B7C2, A0A075B7E2

RefSeq proteins (1): NP_660315* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029174	DUF4637	Domain

Pfam: PF15470

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WW18-F1	58.44	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): HP1SITEFACTOR_Q6, TGGAAA_NFAT_Q4_01, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, CHYLA_CBFA2T3_TARGETS_UP, PEDRIOLI_MIR31_TARGETS_UP, MIR12128, MIR329_5P, MIR4257, chr17q12, GSE15750_WT_VS_TRAF6KO_DAY6_EFF_CD8_TCELL_DN, WP_17Q12_COPY_NUMBER_VARIATION_SYNDROME, GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN, GSE7460_CTRL_VS_FOXP3_OVEREXPR_TCONV_1_UP, GSE9037_CTRL_VS_LPS_1H_STIM_BMDM_DN, GSE2770_TGFB_AND_IL4_VS_TGFB_AND_IL12_TREATED_ACT_CD4_TCELL_2H_UP

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

132 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C17orf50	SPMAP1	A8MV24	693
C17orf50	CFAP97D1	B2RV13	691
C17orf50	SPEM2	Q0P670	668
C17orf50	TBC1D3K	A0A087X1G2	570
C17orf50	KRTAP9-7	A8MTY7	545
C17orf50	CDRT15L2	A8MXV6	507
C17orf50	TBC1D3H	P0C7X1	475
C17orf50	KRTAP9-8	Q9BYQ0	447
C17orf50	TBC1D28	Q2M2D7	445
C17orf50	OR1E2	P47887	433
C17orf50	TBC1D3D	A0A087WVF3	432
C17orf50	SLC35G3	Q8N808	418
C17orf50	SLC35G6	P0C7Q6	418
C17orf50	OR1D5	P58170	417
C17orf50	CCDC144A	A2RUR9	415

IntAct

34 interactions, top by confidence:

A	B	Type	Score
	C17orf50	psi-mi:“MI:0915”(physical association)	0.560
C17orf50	CIB3	psi-mi:“MI:0915”(physical association)	0.560
KRT34	C17orf50	psi-mi:“MI:0915”(physical association)	0.560
C17orf50	CTNNA3	psi-mi:“MI:0915”(physical association)	0.560
C17orf50	ZNF587	psi-mi:“MI:0915”(physical association)	0.560
C17orf50	PCSK5	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	C17orf50	psi-mi:“MI:0915”(physical association)	0.560
VWC2L	C17orf50	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-5	C17orf50	psi-mi:“MI:0915”(physical association)	0.560
ANKS1A	C17orf50	psi-mi:“MI:0915”(physical association)	0.560
	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
KRTAP10-8	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
VWC2L	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
KRTAP10-5	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
ANKS1A	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
CIB3	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
KRT34	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
ZNF587	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
PCSK5	C17orf50	psi-mi:“MI:0915”(physical association)	0.000
CTNNA3	C17orf50	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Two-hybrid), C17orf50 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTK4, A0A1B0GTK5, A0JNL8, A2RUT3, A4D250, B2KGE5, F1MQW7, F2Z3F1, F5HHT4, O93195, O95411, P04610, P05905, P0C733, P0C7M3, P0DP71, P16722, P17758, P47939, P47940, P57738, Q0VD86, Q1HVB5, Q1RN00, Q1X6Y7, Q1X6Z1, Q1X6Z2, Q3ZN08, Q5PR19, Q5PXH1, Q5TC04, Q5TEZ4, Q64902, Q66669, Q66HF0, Q67863, Q6DGF6, Q6UYE1, Q7L4S7, Q8AZJ3

Diamond homologs: Q8C1R3, Q8WW18

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2574697	GRCh37/hg19 17q11.2-12(chr17:30572862-35843988)	Pathogenic

SpliceAI

462 predictions. Top by Δscore:

Variant	Effect	Δscore
17:35764004:CA:C	acceptor_loss	0.9900
17:35764005:A:AG	acceptor_gain	0.9900
17:35764006:G:GG	acceptor_gain	0.9900
17:35764006:GGT:G	acceptor_gain	0.9900
17:35764006:GGTGT:G	acceptor_gain	0.9900
17:35764005:AG:A	acceptor_gain	0.9800
17:35764006:GG:G	acceptor_gain	0.9800
17:35760950:GCATG:G	donor_gain	0.9700
17:35760951:CATGG:C	donor_loss	0.9700
17:35760955:G:GC	donor_loss	0.9700
17:35760956:T:A	donor_loss	0.9700
17:35760955:G:GG	donor_gain	0.9500
17:35763998:G:A	acceptor_gain	0.9500
17:35760953:TG:T	donor_gain	0.9400
17:35760954:GG:G	donor_gain	0.9400
17:35760957:GA:G	donor_loss	0.9400
17:35762764:C:T	donor_gain	0.9300
17:35764005:AGGT:A	acceptor_gain	0.9300
17:35764006:GGTG:G	acceptor_gain	0.9300
17:35764689:T:TA	acceptor_gain	0.9200
17:35764691:G:C	acceptor_gain	0.9200
17:35760946:A:G	donor_gain	0.9100
17:35760951:CATG:C	donor_gain	0.9100
17:35764161:AGCGG:A	donor_gain	0.9100
17:35760945:GA:G	donor_gain	0.9000
17:35764238:T:TA	donor_gain	0.8800
17:35764239:G:GA	donor_gain	0.8800
17:35760952:ATG:A	donor_gain	0.8700
17:35764160:T:TA	donor_gain	0.8700
17:35764240:GCGCT:G	donor_gain	0.8700

AlphaMissense

1116 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:35764514:T:C	F141L	0.978
17:35764516:C:A	F141L	0.978
17:35764516:C:G	F141L	0.978
17:35764518:G:A	C142Y	0.975
17:35764540:C:A	H149Q	0.971
17:35764540:C:G	H149Q	0.971
17:35764026:G:C	W11C	0.969
17:35764026:G:T	W11C	0.969
17:35764517:T:A	C142S	0.968
17:35764518:G:C	C142S	0.968
17:35764579:C:A	H162Q	0.966
17:35764579:C:G	H162Q	0.966
17:35764517:T:C	C142R	0.965
17:35764526:T:A	C145S	0.965
17:35764527:G:C	C145S	0.965
17:35764538:C:G	H149D	0.964
17:35764503:G:A	C137Y	0.961
17:35764519:C:G	C142W	0.958
17:35764564:C:A	H157Q	0.955
17:35764564:C:G	H157Q	0.955
17:35764526:T:C	C145R	0.954
17:35764502:T:A	C137S	0.947
17:35764503:G:C	C137S	0.947
17:35764569:T:A	V159D	0.947
17:35764452:G:A	C120Y	0.944
17:35764518:G:T	C142F	0.943
17:35764451:T:A	C120S	0.942
17:35764452:G:C	C120S	0.942
17:35764515:T:C	F141S	0.941
17:35764024:T:A	W11R	0.938

dbSNP variants (sampled 300 via entrez): RS1002296935 (17:35759657 C>T), RS1002347829 (17:35759820 C>T), RS1002981605 (17:35764357 G>A), RS1004296619 (17:35759886 T>A), RS1004753345 (17:35760144 T>A,C), RS1005463380 (17:35763272 A>C), RS1007148891 (17:35761852 C>T), RS1007481056 (17:35760263 C>T), RS1008534228 (17:35759382 G>A), RS1009453032 (17:35765030 C>A), RS1010891691 (17:35765162 C>A,T), RS1011228620 (17:35764017 C>G,T), RS1011504374 (17:35759441 C>A), RS1013386313 (17:35761770 C>A,G), RS1013468710 (17:35763162 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:614527

GenCC curated gene-disease

Mondo (1): chromosome 17q12 deletion syndrome (MONDO:0013797)

Orphanet (1): 17q12 microdeletion syndrome (Orphanet:261265)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST007001_12	Cerebrospinal AB1-42 levels in normal cognition	4.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004670	beta-amyloid 1-42 measurement

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
Arsenic	affects methylation	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01238250	Not specified	RECRUITING	Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight