C5orf52

Summary

C5orf52 (chromosome 5 open reading frame 52, HGNC:35121) is a protein-coding gene on chromosome 5q33.3, encoding Uncharacterized protein C5orf52 (A6NGY3).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 5 total — 1 pathogenic
• MANE Select transcript: NM_001145132

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:35121
Approved symbol	C5orf52
Name	chromosome 5 open reading frame 52
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187658
Ensembl biotype	protein_coding
Entrez	100190949

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000409999

RefSeq mRNA: 1 — MANE Select: NM_001145132 NM_001145132

CCDS: CCDS47329

Canonical transcript exons

ENST00000409999 — 3 exons

Exon	Start	End
ENSE00001365239	157675092	157675200
ENSE00001577869	157679841	157680158
ENSE00001580984	157671533	157671826

Expression profiles

Bgee: expression breadth broad, 44 present calls, max score 89.54.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1097 / max 83.9018, expressed in 10 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
59834	0.0662	5
59836	0.0243	4
59833	0.0153	3
59835	0.0039	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	89.54	gold quality
right testis	UBERON:0004534	89.48	gold quality
testis	UBERON:0000473	88.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.55	gold quality
mucosa of transverse colon	UBERON:0004991	71.56	gold quality
transverse colon	UBERON:0001157	60.80	gold quality
rectum	UBERON:0001052	60.47	gold quality
duodenum	UBERON:0002114	57.43	gold quality
right uterine tube	UBERON:0001302	50.82	gold quality
colonic epithelium	UBERON:0000397	49.24	silver quality
small intestine	UBERON:0002108	47.13	gold quality
small intestine Peyer’s patch	UBERON:0003454	47.00	gold quality
intestine	UBERON:0000160	46.40	gold quality
colon	UBERON:0001155	46.33	gold quality
granulocyte	CL:0000094	42.64	silver quality
fallopian tube	UBERON:0003889	42.58	gold quality
prefrontal cortex	UBERON:0000451	37.29	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
hypothalamus	UBERON:0001898	35.96	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
frontal cortex	UBERON:0001870	34.07	silver quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
metanephros cortex	UBERON:0010533	32.66	gold quality
anterior cingulate cortex	UBERON:0009835	32.25	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
cerebral cortex	UBERON:0000956	32.03	silver quality
liver	UBERON:0002107	31.99	gold quality
bone marrow	UBERON:0002371	31.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting C5orf52, 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-139-5P	99.80	69.50	1399
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-6739-3P	99.22	68.84	1843

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	4921536K21Rik	ENSMUSG00000020434
rattus_norvegicus	C14h5orf52	ENSRNOG00000004112

Protein

Protein identifiers

Uncharacterized protein C5orf52 — A6NGY3 (reviewed: A6NGY3)

All UniProt accessions (1): A6NGY3

RefSeq proteins (1): NP_001138604* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038935	C5orf52	Family

Pfam: PF17666

UniProt features (5 total): compositionally biased region 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NGY3-F1	75.49	0.36

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN, ATF5_TARGET_GENES, DMRT1_TARGET_GENES, LMX1B_TARGET_GENES, ZFHX3_TARGET_GENES, ZNF407_TARGET_GENES, GSE13493_CD4INTCD8POS_VS_CD8POS_THYMOCYTE_UP, GSE17721_CTRL_VS_LPS_4H_BMDC_DN, chr5q33, GSE17721_PAM3CSK4_VS_GADIQUIMOD_12H_BMDC_DN, DESCARTES_FETAL_INTESTINE_INTESTINAL_EPITHELIAL_CELLS, GSE17721_LPS_VS_GARDIQUIMOD_12H_BMDC_DN, TOX4_TARGET_GENES, LHX2_TARGET_GENES, ZNF260_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

132 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C5orf52	CFAP97D1	B2RV13	610
C5orf52	TMEM42	Q69YG0	541
C5orf52	CCDC24	Q8N4L8	515
C5orf52	SPMIP9	Q96LM6	507
C5orf52	TLCD5	Q6ZRR5	507
C5orf52	CCDC116	Q8IYX3	506
C5orf52	KIAA0586	Q9BVV6	506
C5orf52	DNAJC5G	Q8N7S2	476
C5orf52	FBXW12	Q6X9E4	448
C5orf52	DDX59	Q5T1V6	448
C5orf52	TMEM67	Q5HYA8	419
C5orf52	SNX29	Q8TEQ0	398
C5orf52	NIBAN2	Q96TA1	397
C5orf52	KIAA0753	Q2KHM9	366
C5orf52	STK10	O94804	323

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GU33, A0A1B0GUV7, A6NGY3, A6ZT44, F5HHT4, G2TRR6, H3BU77, O13894, O54835, O89085, P0C2W9, P0C6G1, P0C6G2, P0C6G3, P0C6G4, P0C6G5, P0C733, P0DON5, P0DON6, P14976, P16722, P27262, P27271, P28979, P29887, P38612, P38839, Q05105, Q08588, Q1KN14, Q1KN19, Q1X6Y3, Q1X6Y4, Q1X6Z0, Q2YDL7, Q5R5R7, Q5ZK14, Q67621, Q6W0C5, Q88891

Diamond homologs: A6NGY3, Q9CR34

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
684880	GRCh37/hg19 5q33.3-35.1(chr5:156597181-171166353)x3	Pathogenic

SpliceAI

495 predictions. Top by Δscore:

Variant	Effect	Δscore
5:157679838:AAGGT:A	acceptor_gain	1.0000
5:157671876:G:T	donor_gain	0.9900
5:157679835:T:TA	acceptor_gain	0.9900
5:157679838:A:AG	acceptor_gain	0.9900
5:157679838:AAG:A	acceptor_gain	0.9900
5:157679839:A:AG	acceptor_loss	0.9900
5:157679839:A:G	acceptor_gain	0.9900
5:157671766:G:GT	donor_gain	0.9800
5:157679839:AGGTG:A	acceptor_gain	0.9800
5:157679840:GGT:G	acceptor_gain	0.9800
5:157679839:AGGT:A	acceptor_gain	0.9700
5:157679840:G:A	acceptor_gain	0.9700
5:157679840:GGTG:G	acceptor_gain	0.9700
5:157679840:GGTGA:G	acceptor_gain	0.9700
5:157671845:GAGC:G	donor_gain	0.9600
5:157672160:GGGGA:G	donor_gain	0.9600
5:157679840:G:GG	acceptor_gain	0.9600
5:157671771:C:A	donor_gain	0.9400
5:157671823:TCAG:T	donor_loss	0.9400
5:157671824:CAG:C	donor_loss	0.9400
5:157671825:AGG:A	donor_loss	0.9400
5:157671826:GG:G	donor_loss	0.9400
5:157671827:G:A	donor_loss	0.9400
5:157671828:T:G	donor_loss	0.9400
5:157671941:A:T	donor_gain	0.9400
5:157672257:G:GA	donor_gain	0.9300
5:157671819:C:CG	donor_gain	0.9200
5:157679839:AG:A	acceptor_gain	0.9200
5:157671759:GGC:G	donor_gain	0.9100
5:157671760:GCG:G	donor_gain	0.9100

AlphaMissense

1034 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:157679904:T:C	F129L	0.979
5:157679906:C:A	F129L	0.979
5:157679906:C:G	F129L	0.979
5:157679897:A:C	K126N	0.964
5:157679897:A:T	K126N	0.964
5:157679893:T:C	L125P	0.953
5:157679905:T:C	F129S	0.947
5:157671786:T:C	F58L	0.943
5:157671788:T:A	F58L	0.943
5:157671788:T:G	F58L	0.943
5:157679939:G:C	W140C	0.933
5:157679939:G:T	W140C	0.933
5:157679937:T:A	W140R	0.926
5:157679937:T:C	W140R	0.926
5:157671822:T:C	F70L	0.923
5:157671824:C:A	F70L	0.923
5:157671824:C:G	F70L	0.923
5:157675166:A:T	D96V	0.920
5:157679927:G:C	K136N	0.919
5:157679927:G:T	K136N	0.919
5:157679896:A:T	K126I	0.918
5:157675138:A:C	S87R	0.911
5:157675140:C:A	S87R	0.911
5:157675140:C:G	S87R	0.911
5:157679917:A:C	Q133P	0.907
5:157675145:T:C	L89S	0.906
5:157675157:T:C	I93T	0.897
5:157671825:A:C	S71R	0.892
5:157675092:C:A	S71R	0.892
5:157675092:C:G	S71R	0.892

dbSNP variants (sampled 300 via entrez): RS1000146346 (5:157673952 A>G,T), RS1000272919 (5:157672241 C>T), RS1000397292 (5:157677595 G>A,C,T), RS1000874291 (5:157673452 A>G), RS1001005869 (5:157679009 A>C,G), RS1002712321 (5:157670543 G>A), RS1002851424 (5:157675845 A>G), RS1003093027 (5:157678130 C>T), RS1003499353 (5:157676951 C>T), RS1003684615 (5:157671615 A>G), RS1003834596 (5:157676520 A>G,T), RS1004113047 (5:157680002 T>A,C), RS1004360709 (5:157674078 A>G), RS1004674191 (5:157669727 G>C,T), RS1004874379 (5:157676486 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
GCST011066_3	Motor fluctuations in levodopa treated Parkinson’s disease	9.000000e-06
GCST011766_9	Chronic obstructive pulmonary disease	1.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010747	response to levodopa
EFO:0010749	motor function 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
Benzo(a)pyrene	increases methylation	1

Clinical trials (associated diseases)

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