C22orf42

Summary

C22orf42 (chromosome 22 open reading frame 42, HGNC:27160) is a protein-coding gene on chromosome 22q12.3, encoding Uncharacterized protein C22orf42 (Q6IC83).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_001010859

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27160
Approved symbol	C22orf42
Name	chromosome 22 open reading frame 42
Location	22q12.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205856
Ensembl biotype	protein_coding
Entrez	150297

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000382097, ENST00000467813, ENST00000490640

RefSeq mRNA: 1 — MANE Select: NM_001010859 NM_001010859

CCDS: CCDS33639

Canonical transcript exons

ENST00000382097 — 9 exons

Exon	Start	End
ENSE00003994208	32150319	32150479
ENSE00003994209	32158984	32159303
ENSE00003994210	32149006	32149613
ENSE00003994211	32152067	32152094
ENSE00003994213	32151487	32151551
ENSE00003994215	32154244	32154318
ENSE00003994216	32149753	32149780
ENSE00003994218	32152562	32152626
ENSE00003994219	32150992	32151019

Expression profiles

Bgee: expression breadth broad, 100 present calls, max score 94.20.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1201 / max 60.1886, expressed in 29 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193737	0.1078	27
193736	0.0124	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.20	gold quality
islet of Langerhans	UBERON:0000006	84.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.85	gold quality
buccal mucosa cell	CL:0002336	83.50	gold quality
right testis	UBERON:0004534	82.81	gold quality
left testis	UBERON:0004533	82.65	gold quality
testis	UBERON:0000473	79.76	gold quality
hypothalamus	UBERON:0001898	74.49	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	70.23	gold quality
pancreas	UBERON:0001264	63.07	gold quality
pituitary gland	UBERON:0000007	58.56	gold quality
adenohypophysis	UBERON:0002196	58.41	gold quality
prostate gland	UBERON:0002367	54.20	gold quality
body of pancreas	UBERON:0001150	53.88	gold quality
upper leg skin	UBERON:0004262	51.90	silver quality
cortical plate	UBERON:0005343	50.50	gold quality
colonic epithelium	UBERON:0000397	50.42	gold quality
adult organism	UBERON:0007023	49.78	silver quality
right lobe of liver	UBERON:0001114	49.31	gold quality
lower esophagus mucosa	UBERON:0035834	49.16	gold quality
substantia nigra	UBERON:0002038	48.06	gold quality
midbrain	UBERON:0001891	47.05	gold quality
gastrocnemius	UBERON:0001388	46.54	gold quality
cerebellar vermis	UBERON:0004720	46.54	gold quality
muscle of leg	UBERON:0001383	46.23	gold quality
leukocyte	CL:0000738	45.72	silver quality
skin of hip	UBERON:0001554	45.62	silver quality
monocyte	CL:0000576	45.38	silver quality
liver	UBERON:0002107	44.04	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-81547	yes	692.11
E-MTAB-5061	yes	11.13
E-ANND-3	no	1.95

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (1): DRICH1 (ENSG00000189269)

Protein

Protein identifiers

Uncharacterized protein C22orf42 — Q6IC83 (reviewed: Q6IC83)

All UniProt accessions (1): Q6IC83

RefSeq proteins (1): NP_001010859* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR042865	DRICH1-like	Family

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6IC83-F1	52.61	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): chr22q12, MANNO_MIDBRAIN_NEUROTYPES_HNBML5, MANNO_MIDBRAIN_NEUROTYPES_HDA, MANNO_MIDBRAIN_NEUROTYPES_HDA2, MANNO_MIDBRAIN_NEUROTYPES_HNBGABA, MANNO_MIDBRAIN_NEUROTYPES_HSERT, DESCARTES_MAIN_FETAL_ISLET_ENDOCRINE_CELLS, DESCARTES_FETAL_PANCREAS_ISLET_ENDOCRINE_CELLS, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_24H_ACT_CD4_TCELL_UP, VANGURP_PANCREATIC_DELTA_CELL, GSE6566_STRONG_VS_WEAK_DC_STIMULATED_CD4_TCELL_UP, GSE2128_CTRL_VS_MIMETOPE_NEGATIVE_SELECTION_DP_THYMOCYTE_C57BL6_UP, GSE19198_CTRL_VS_IL21_TREATED_TCELL_1H_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

208 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C22orf42	C3orf22	Q8N5N4	590
C22orf42	RNASE12	Q5GAN4	569
C22orf42	C12orf56	Q8IXR9	544
C22orf42	SMIM17	P0DL12	540
C22orf42	DRICH1	Q6PGQ1	507
C22orf42	SH2D7	A6NKC9	507
C22orf42	ANKRD62	A6NC57	507
C22orf42	C1orf167	Q5SNV9	507
C22orf42	CC2D2B	Q6DHV5	507
C22orf42	SPDYE4	A6NLX3	495
C22orf42	FAM131C	Q96AQ9	480
C22orf42	CLPSL1	A2RUU4	479
C22orf42	EPCIP	Q9NYP8	478
C22orf42	RD3L	P0DJH9	477
C22orf42	SMIM21	Q3B7S5	476

IntAct

5 interactions, top by confidence:

A	B	Type	Score
rep	C22orf42	psi-mi:“MI:0915”(physical association)	0.490
C22orf42	H1-1	psi-mi:“MI:0915”(physical association)	0.400
C22orf42	CYB5R3	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): C22orf42 (Proximity Label-MS), GNPTG (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), ANKRD13D (Affinity Capture-MS), WDR44 (Affinity Capture-MS), CYB5R3 (Affinity Capture-MS), EPHA5 (Affinity Capture-MS), CERK (Affinity Capture-MS), SEPT14 (Affinity Capture-MS), ANKRD13A (Affinity Capture-MS), C22orf42 (Affinity Capture-MS), C22orf42 (Two-hybrid)

ESM2 similar proteins: A0A1D9BZF0, A6QL64, B4DH59, B5DUH6, D3YZV8, E9Q6E9, O43493, O46383, O77733, P06916, P08116, P0C758, P0DKJ7, P0DKJ8, P0DPF3, P31568, P62521, Q01033, Q01042, Q1HVF7, Q2W8Q7, Q3BBV2, Q42626, Q42627, Q4ZJZ1, Q4ZJZ3, Q5JPF3, Q5MJ10, Q6AXX0, Q6GX35, Q6IC83, Q6P3W6, Q6PGQ1, Q7M4S9, Q7M732, Q86T75, Q8BP27, Q8IZU1, Q8N2N9, Q96QF7

Diamond homologs: Q6IC83, Q6PGQ1, D3YUJ3, Q8N7R7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1190 predictions. Top by Δscore:

Variant	Effect	Δscore
22:32149751:A:AC	donor_gain	1.0000
22:32149752:C:CC	donor_gain	1.0000
22:32150317:A:AC	donor_gain	1.0000
22:32150318:C:CC	donor_gain	1.0000
22:32150318:CCAT:C	donor_gain	1.0000
22:32150475:CAAAT:C	acceptor_gain	1.0000
22:32150480:C:CC	acceptor_gain	1.0000
22:32150990:A:AC	donor_gain	1.0000
22:32150991:C:CC	donor_gain	1.0000
22:32151485:A:AC	donor_gain	1.0000
22:32151486:C:CC	donor_gain	1.0000
22:32151549:GACC:G	acceptor_loss	1.0000
22:32151551:CCTAG:C	acceptor_loss	1.0000
22:32151552:CTAG:C	acceptor_loss	1.0000
22:32151553:T:C	acceptor_loss	1.0000
22:32152065:A:AC	donor_gain	1.0000
22:32152066:C:CC	donor_gain	1.0000
22:32152100:A:AC	acceptor_gain	1.0000
22:32152560:A:AC	donor_gain	1.0000
22:32152561:C:CC	donor_gain	1.0000
22:32152566:T:C	donor_gain	1.0000
22:32152625:ACCTA:A	acceptor_loss	1.0000
22:32152626:CCTAG:C	acceptor_loss	1.0000
22:32152627:C:CC	acceptor_gain	1.0000
22:32152627:C:CG	acceptor_loss	1.0000
22:32158979:TTTAC:T	donor_loss	1.0000
22:32158980:TTA:T	donor_loss	1.0000
22:32158981:TACCT:T	donor_loss	1.0000
22:32158982:A:C	donor_loss	1.0000
22:32158983:C:CG	donor_loss	1.0000

AlphaMissense

1662 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:32150382:G:C	F197L	0.871
22:32150382:G:T	F197L	0.871
22:32150384:A:G	F197L	0.871
22:32149609:C:A	W229C	0.857
22:32149609:C:G	W229C	0.857
22:32150430:G:C	F181L	0.846
22:32150430:G:T	F181L	0.846
22:32150432:A:G	F181L	0.846
22:32149599:C:G	A233P	0.831
22:32154280:A:G	W91R	0.830
22:32154280:A:T	W91R	0.830
22:32154295:A:G	W86R	0.820
22:32154295:A:T	W86R	0.820
22:32154278:C:A	W91C	0.817
22:32154278:C:G	W91C	0.817
22:32154299:C:A	K84N	0.812
22:32154299:C:G	K84N	0.812
22:32149611:A:G	W229R	0.794
22:32149611:A:T	W229R	0.794
22:32154275:T:A	R92S	0.792
22:32154275:T:G	R92S	0.792
22:32154264:A:G	I96T	0.787
22:32159188:C:G	G10R	0.750
22:32154291:A:G	L87S	0.749
22:32154273:C:G	R93P	0.742
22:32154262:A:G	W97R	0.728
22:32154262:A:T	W97R	0.728
22:32159165:A:C	C17W	0.715
22:32154279:C:G	W91S	0.711
22:32154268:C:A	G95W	0.709

dbSNP variants (sampled 300 via entrez): RS1000445492 (22:32151168 G>T), RS1000790654 (22:32157330 A>C,G), RS1000962915 (22:32149921 C>A,T), RS1001353674 (22:32158592 T>C), RS1001381628 (22:32149540 C>T), RS1001500515 (22:32157974 G>A), RS1001679947 (22:32151810 A>T), RS1002349043 (22:32150227 T>C), RS1002603001 (22:32159710 C>T), RS1002713779 (22:32152713 G>A,T), RS1003608446 (22:32160766 A>C), RS1003795730 (22:32148984 G>T), RS1003948560 (22:32150636 G>A), RS1004263465 (22:32162383 G>A), RS1004463234 (22:32149987 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
GCST003814_21	Selective IgA deficiency	4.000000e-06
GCST010315_3	Serum linoleic acid concentration in metabolic syndrome	1.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006807	linoleic acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation	2
ethyl-p-hydroxybenzoate	decreases expression	1
trichostatin A	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
pentanal	increases expression	1
clothianidin	decreases expression	1
Arsenic Trioxide	increases expression	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Methapyrilene	increases methylation	1
Valproic Acid	increases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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