C20orf204

Summary

C20orf204 (chromosome 20 open reading frame 204, HGNC:27655) is a protein-coding gene on chromosome 20q13.33, encoding Uncharacterized protein C20orf204 (A0A1B0GTL2).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 5 total — 1 pathogenic
• MANE Select transcript: NM_001387010

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27655
Approved symbol	C20orf204
Name	chromosome 20 open reading frame 204
Location	20q13.33
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434G015, FLJ27267
Ensembl gene	ENSG00000196421
Ensembl biotype	protein_coding
Entrez	284739

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 retained_intron, 2 protein_coding

ENST00000358393, ENST00000431158, ENST00000444463, ENST00000463337, ENST00000636176

RefSeq mRNA: 2 — MANE Select: NM_001387010 NM_001348090, NM_001387010

CCDS: CCDS86971

Canonical transcript exons

ENST00000636176 — 4 exons

Exon	Start	End
ENSE00003794348	64038622	64039001
ENSE00003794589	64036182	64036326
ENSE00003798161	64038296	64038448
ENSE00003798949	64037927	64038202

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 85.86.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0890 / max 99.8908, expressed in 229 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
185917	0.3556	117
185915	0.2301	41
185918	0.1796	84
185919	0.1020	51
185920	0.0826	31
185921	0.0690	33
185913	0.0257	15
185914	0.0244	9
185916	0.0201	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	85.86	gold quality
pancreatic ductal cell	CL:0002079	85.55	silver quality
cerebellar hemisphere	UBERON:0002245	85.41	gold quality
cerebellar cortex	UBERON:0002129	85.27	gold quality
cerebellum	UBERON:0002037	83.60	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.34	silver quality
epithelial cell of pancreas	CL:0000083	72.05	gold quality
right uterine tube	UBERON:0001302	71.97	gold quality
tendon of biceps brachii	UBERON:0008188	66.46	silver quality
pituitary gland	UBERON:0000007	65.91	gold quality
adenohypophysis	UBERON:0002196	65.60	gold quality
kidney epithelium	UBERON:0004819	65.41	gold quality
cortical plate	UBERON:0005343	64.94	gold quality
vena cava	UBERON:0004087	64.69	gold quality
sural nerve	UBERON:0015488	64.48	silver quality
upper arm skin	UBERON:0004263	63.78	gold quality
left ovary	UBERON:0002119	62.49	gold quality
right frontal lobe	UBERON:0002810	61.74	gold quality
nucleus accumbens	UBERON:0001882	61.11	gold quality
bone marrow cell	CL:0002092	61.08	gold quality
cerebellar vermis	UBERON:0004720	60.88	gold quality
ganglionic eminence	UBERON:0004023	60.78	gold quality
right ovary	UBERON:0002118	59.83	gold quality
tibial nerve	UBERON:0001323	59.73	gold quality
amniotic fluid	UBERON:0000173	59.58	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	59.56	gold quality
hypothalamus	UBERON:0001898	59.47	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	59.40	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	59.38	gold quality
putamen	UBERON:0001874	59.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.42

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• Study identified a novel long intergenic noncoding RNA, Linc00176, that plays a role in proliferation and survival of hepatocellular carcinoma. (PMID:28869604)
• Knockdown of long non-coding RNA LINC00176 suppresses ovarian cancer progression by BCL3-mediated down-regulation of ceruloplasmin. (PMID:31668012)
• LINC00176 facilitates CD4(+)T cell adhesion in systemic lupus erythematosus via the WNT5a signaling pathway by regulating WIF1. (PMID:33813201)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm29797	ENSMUSG00000108976

Protein

Protein identifiers

Uncharacterized protein C20orf204 — A0A1B0GTL2 (reviewed: A0A1B0GTL2)

All UniProt accessions (2): A0A1B0GTL2, A0A1B0GVI8

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (2): NP_001335019, NP_001373939* (*=MANE)

Domains & families (InterPro)

UniProt features (3 total): signal peptide 1, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GTL2-F1	71.16	0.26

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 72

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, RYTTCCTG_ETS2_B, PIT1_Q6, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, MARTENS_TRETINOIN_RESPONSE_DN, NFKBIA_TARGET_GENES, ZNF597_TARGET_GENES, BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_UP, DESCARTES_FETAL_HEART_LYMPHATIC_ENDOTHELIAL_CELLS, DESCARTES_FETAL_PANCREAS_LYMPHATIC_ENDOTHELIAL_CELLS, HDGF_TARGET_GENES, TCF1P_Q6, HE_LIM_SUN_FETAL_LUNG_C3_INTERMEDIATE_LYMPHATIC_ENDO_CELL, HE_LIM_SUN_FETAL_LUNG_C3_LYMPHATIC_ENDOTHELIAL_CELL

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

58 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C20orf204	MTLN	Q8NCU8	573
C20orf204	BICDL2	A1A5D9	543
C20orf204	KRT78	Q8N1N4	399
C20orf204	MRGBP	Q9NV56	394
C20orf204	TMBIM4	Q9HC24	392
C20orf204	DBT	P11182	348
C20orf204	TMED10	P49755	343
C20orf204	NUCLEOLIN	P19338	334
C20orf204	MAB21L4	Q08AI8	321
C20orf204	OLFM1	Q99784	320
C20orf204	SRSF10	O75494	309
C20orf204	TMTC1	Q8IUR5	306
C20orf204	PTBP2	Q9UKA9	299
C20orf204	SPINK8	P0C7L1	290
C20orf204	GFOD2	Q3B7J2	288

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A140LIA7, A0A1B0GTL2, A2VDX9, A3FFS8, A6NCS6, A8MVW0, K9M1U5, O43541, P01588, P03971, P03972, P07321, P07865, P0C7N4, P0DPE3, P13725, P27106, P29676, P33707, P33708, P33709, P48617, P49000, P49157, P53346, P79295, Q02011, Q0Z956, Q16619, Q1HCM0, Q28513, Q29RM6, Q5BLP8, Q5S1V9, Q60753, Q63086, Q65Z15, Q6H8S9, Q6H8T0, Q6H8T1

Diamond homologs: A0A140LIA7, A0A1B0GTL2

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	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
147280	GRCh38/hg38 20q13.33(chr20:64023324-64261777)x1	Pathogenic

SpliceAI

123 predictions. Top by Δscore:

Variant	Effect	Δscore
20:64038309:T:TA	donor_gain	0.9600
20:64038305:ATCCT:A	donor_gain	0.9300
20:64038324:C:A	donor_gain	0.8700
20:64038305:AT:A	donor_gain	0.8300
20:64039097:T:TA	donor_gain	0.8300
20:64038389:TGG:T	donor_gain	0.8200
20:64038602:G:T	donor_gain	0.7900
20:64038701:TCGCC:T	donor_gain	0.7900
20:64038286:C:A	donor_gain	0.7800
20:64038705:C:CT	donor_gain	0.7800
20:64038704:C:CT	donor_gain	0.7600
20:64038483:C:A	donor_gain	0.7400
20:64038306:T:TA	donor_gain	0.7300
20:64038825:G:A	donor_gain	0.7300
20:64038558:C:CA	donor_gain	0.7000
20:64037936:AAG:A	donor_gain	0.6600
20:64038291:C:A	donor_gain	0.6600
20:64037932:C:CA	donor_gain	0.6500
20:64039004:C:CA	donor_gain	0.6400
20:64039098:C:A	donor_gain	0.6300
20:64034635:T:TG	acceptor_gain	0.6100
20:64038645:C:CA	donor_gain	0.6000
20:64038677:T:TA	donor_gain	0.5900
20:64038769:T:TA	donor_gain	0.5800
20:64038281:C:CA	donor_gain	0.5700
20:64038488:AACC:A	donor_gain	0.5700
20:64038563:C:A	donor_gain	0.5700
20:64038488:AACCC:A	donor_gain	0.5500
20:64038512:C:A	donor_gain	0.5500
20:64038562:T:TA	donor_gain	0.5300

AlphaMissense

1176 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:64038714:G:C	W175C	0.992
20:64038714:G:T	W175C	0.992
20:64038318:T:A	I101N	0.982
20:64038306:T:C	I97T	0.979
20:64038318:T:C	I101T	0.979
20:64038712:T:A	W175R	0.977
20:64038712:T:C	W175R	0.977
20:64038724:T:C	F179L	0.977
20:64038726:C:A	F179L	0.977
20:64038726:C:G	F179L	0.977
20:64038318:T:G	I101S	0.971
20:64038047:T:C	F42L	0.967
20:64038049:C:A	F42L	0.967
20:64038049:C:G	F42L	0.967
20:64038716:A:T	E176V	0.965
20:64038711:C:G	C174W	0.964
20:64038710:G:A	C174Y	0.963
20:64038054:A:T	D44V	0.961
20:64038399:C:A	A128D	0.961
20:64038045:T:C	I41T	0.959
20:64038057:T:C	L45P	0.957
20:64038306:T:G	I97S	0.957
20:64038053:G:C	D44H	0.956
20:64038054:A:C	D44A	0.956
20:64038398:G:C	A128P	0.956
20:64038306:T:A	I97N	0.955
20:64038045:T:A	I41N	0.954
20:64038701:T:A	V171D	0.954
20:64038709:T:C	C174R	0.954
20:64038054:A:G	D44G	0.945

dbSNP variants (sampled 300 via entrez): RS1000050189 (20:64034563 G>A), RS1000245292 (20:64039461 C>T), RS1000853749 (20:64037850 CAA>C,CAAA), RS1000981948 (20:64033074 TAA>T,TA), RS1001307256 (20:64037502 G>A,T), RS1001342758 (20:64039139 C>G), RS1001393757 (20:64039413 C>A), RS1001602990 (20:64033412 C>T), RS1001849064 (20:64033654 C>T), RS1001882709 (20:64032494 C>T), RS1002169099 (20:64033915 T>A), RS1002368941 (20:64037225 G>A), RS1002699662 (20:64036105 C>G,T), RS1003064052 (20:64038220 C>G,T), RS1003343707 (20:64036700 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

1 associations (top):

Study	Trait	p-value
GCST007001_16	Cerebrospinal AB1-42 levels in normal cognition	3.000000e-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

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

Chemical	Actions (top 5)	PubMed papers
Estradiol	decreases expression	2
Tetrachlorodibenzodioxin	increases expression	2
aristolochic acid I	increases expression	1
ferrous chloride	decreases expression	1
bromovanin	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Dimethyl Sulfoxide	decreases expression	1
Methotrexate	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Triiodothyronine	decreases expression	1
Aflatoxin B1	affects expression	1
Okadaic Acid	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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