C13orf42

Summary

C13orf42 (chromosome 13 open reading frame 42, HGNC:42693) is a protein-coding gene on chromosome 13q14.3, encoding Uncharacterized protein C13orf42 (A0A1B0GVH6).

At a glance

• GWAS associations: 3
• MANE Select transcript: NM_001351589

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:42693
Approved symbol	C13orf42
Name	chromosome 13 open reading frame 42
Location	13q14.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000226792
Ensembl biotype	protein_coding
Entrez	647166

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000433280, ENST00000563710, ENST00000569306, ENST00000636098

RefSeq mRNA: 1 — MANE Select: NM_001351589 NM_001351589

CCDS: CCDS86352

Canonical transcript exons

ENST00000563710 — 4 exons

Exon	Start	End
ENSE00001802918	51110796	51111274
ENSE00002617847	51082119	51084325
ENSE00003795854	51087928	51088075
ENSE00003795862	51085319	51085559

Expression profiles

Bgee: expression breadth broad, 52 present calls, max score 86.06.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0413 / max 11.4203, expressed in 20 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
137370	0.0413	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.06	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.01	silver quality
cerebellar vermis	UBERON:0004720	73.66	gold quality
quadriceps femoris	UBERON:0001377	69.42	gold quality
thymus	UBERON:0002370	63.49	silver quality
colonic epithelium	UBERON:0000397	58.36	gold quality
mucosa of stomach	UBERON:0001199	50.86	gold quality
spleen	UBERON:0002106	47.29	gold quality
adenohypophysis	UBERON:0002196	46.49	gold quality
testis	UBERON:0000473	46.01	gold quality
pituitary gland	UBERON:0000007	45.91	gold quality
right testis	UBERON:0004534	45.75	gold quality
left testis	UBERON:0004533	44.00	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	40.81	gold quality
temporal lobe	UBERON:0001871	40.23	gold quality
amygdala	UBERON:0001876	40.07	gold quality
prefrontal cortex	UBERON:0000451	38.89	silver quality
granulocyte	CL:0000094	38.59	gold quality
ganglionic eminence	UBERON:0004023	37.17	gold quality
calcaneal tendon	UBERON:0003701	37.01	gold quality
Ammon’s horn	UBERON:0001954	36.59	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
gall bladder	UBERON:0002110	35.78	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.64	gold quality
placenta	UBERON:0001987	35.42	gold quality
skeletal muscle tissue	UBERON:0001134	35.20	gold quality
subcutaneous adipose tissue	UBERON:0002190	34.90	gold quality
frontal cortex	UBERON:0001870	34.51	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.57
E-MTAB-6058	no	10.78

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm4131	ENSMUSG00000100486
rattus_norvegicus	C15h13orf42	ENSRNOG00000070558

Protein

Protein identifiers

Uncharacterized protein C13orf42 — A0A1B0GVH6 (reviewed: A0A1B0GVH6)

All UniProt accessions (1): A0A1B0GVH6

RefSeq proteins (1): NP_001338518* (*=MANE)

Domains & families (InterPro)

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GVH6-F1	52.75	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr13q14

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

18 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C13orf42	STON1	Q9Y6Q2	593
C13orf42	BBS9	P78514	398
C13orf42	EIF4G3	O43432	394
C13orf42	ADGRV1	Q8WXG9	359
C13orf42	ZBTB20	Q9HC78	356
C13orf42	FHIT	P49789	272
C13orf42	TP63	Q9H3D4	250
C13orf42	RYR2	Q92736	223
C13orf42	WLS	Q5T9L3	174

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A140LFM6, A0A1B0GVH6, A0A1L8H8C0, A0A2K1JJ00, A0JMD2, A2ARZ3, A2AWL7, A4IGV6, A6H5Y1, D3ZJ47, E9Q309, F1QPR4, F5H4B4, H0WFA5, O14513, O35413, O94875, P0CAX8, P48437, Q12912, Q15468, Q1LXZ9, Q1X8D7, Q28FG2, Q3UTJ2, Q3ZBS1, Q499E5, Q49A88, Q4V7H1, Q5T5U3, Q5VT06, Q62417, Q62770, Q69Z38, Q6DFB0, Q80TY4, Q8BLN6, Q8CB14, Q8IWI9, Q8K0T7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2142 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:51085521:A:G	W201R	0.996
13:51085521:A:T	W201R	0.996
13:51110935:A:G	L92P	0.993
13:51110924:G:T	R96S	0.992
13:51110944:A:G	L89P	0.989
13:51085382:A:G	L247S	0.987
13:51085519:C:A	W201C	0.987
13:51085519:C:G	W201C	0.987
13:51110923:C:G	R96P	0.987
13:51110923:C:A	R96L	0.986
13:51085549:G:C	S191R	0.984
13:51085549:G:T	S191R	0.984
13:51085551:T:G	S191R	0.984
13:51085379:G:T	P248H	0.983
13:51111102:G:C	S36R	0.979
13:51111102:G:T	S36R	0.979
13:51111104:T:G	S36R	0.979
13:51085520:C:G	W201S	0.978
13:51085522:G:C	N200K	0.978
13:51085522:G:T	N200K	0.978
13:51110915:A:C	Y99D	0.978
13:51088027:C:G	A155P	0.977
13:51085375:C:A	K249N	0.976
13:51085375:C:G	K249N	0.976
13:51085380:G:T	P248T	0.976
13:51088011:T:A	D160V	0.976
13:51085396:C:A	R242S	0.975
13:51085396:C:G	R242S	0.975
13:51085380:G:A	P248S	0.972
13:51085343:A:G	F260S	0.971

dbSNP variants (sampled 300 via entrez): RS1000002405 (13:51142808 A>C), RS1000060831 (13:51101751 T>C), RS1000116204 (13:51108038 G>C), RS1000119009 (13:51163113 G>A), RS1000151647 (13:51119016 G>T), RS1000160233 (13:51124435 A>C), RS1000201993 (13:51125576 A>C,G), RS1000231855 (13:51136128 C>A,T), RS1000318932 (13:51112904 C>G), RS1000363138 (13:51155027 T>C), RS1000365982 (13:51088067 G>A), RS1000394637 (13:51087814 G>A), RS1000413516 (13:51102069 C>T), RS1000430008 (13:51161241 T>A), RS1000435114 (13:51154827 C>A,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

3 associations (top):

Study	Trait	p-value
GCST007978_3	Postoperative atrial fibrillation after cardiac surgery	1.000000e-06
GCST009464_19	Facial morphology	1.000000e-08
GCST012166_7	Adiponectin levels	8.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0009951	response to surgery
EFO:0009952	post-operative atrial fibrillation
EFO:0004502	adiponectin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
benzo(e)pyrene	increases methylation	1
Methapyrilene	increases methylation	1
Thiram	increases expression	1
Aflatoxin B1	increases methylation	1
Permethrin	increases expression	1

Clinical trials (associated diseases)

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