C20orf173

Summary

C20orf173 (chromosome 20 open reading frame 173, HGNC:16166) is a protein-coding gene on chromosome 20q11.22, encoding Uncharacterized protein C20orf173 (Q96LM9).

Predicted to enable beta-galactoside (CMP) alpha-2,3-sialyltransferase activity. Predicted to be involved in ganglioside biosynthetic process via lactosylceramide; protein glycosylation; and sialylation. Predicted to be active in membrane.

Source: NCBI Gene 140873 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 3 total — 1 pathogenic
• MANE Select transcript: NM_001145350

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16166
Approved symbol	C20orf173
Name	chromosome 20 open reading frame 173
Location	20q11.22
Locus type	gene with protein product
Status	Approved
Aliases	dJ477O4.4
Ensembl gene	ENSG00000125975
Ensembl biotype	protein_coding
Entrez	140873

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000246199, ENST00000374345, ENST00000424444, ENST00000444723

RefSeq mRNA: 1 — MANE Select: NM_001145350 NM_001145350

CCDS: CCDS46594

Canonical transcript exons

ENST00000444723 — 6 exons

Exon	Start	End
ENSE00003462672	35528451	35528544
ENSE00003527122	35529559	35529652
ENSE00003561773	35529065	35529424
ENSE00003580128	35528701	35528879
ENSE00003654878	35528233	35528284
ENSE00003898732	35526979	35527250

Expression profiles

Bgee: expression breadth broad, 27 present calls, max score 98.77.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0313 / max 32.9292, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
187060	0.0313	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	98.77	gold quality
right testis	UBERON:0004534	89.04	gold quality
left testis	UBERON:0004533	88.80	gold quality
testis	UBERON:0000473	88.11	gold quality
granulocyte	CL:0000094	42.62	silver quality
bone marrow cell	CL:0002092	41.49	gold quality
bone marrow	UBERON:0002371	37.62	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
sural nerve	UBERON:0015488	36.87	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	36.25	silver quality
mucosa of stomach	UBERON:0001199	36.17	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
superior frontal gyrus	UBERON:0002661	35.21	gold quality
tonsil	UBERON:0002372	33.14	gold quality
blood	UBERON:0000178	32.30	gold quality
lymph node	UBERON:0000029	31.47	silver quality
primary visual cortex	UBERON:0002436	30.88	gold quality
leukocyte	CL:0000738	29.91	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
uterine cervix	UBERON:0000002	29.70	gold quality
monocyte	CL:0000576	29.30	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	29.24	gold quality
endocervix	UBERON:0000458	29.19	gold quality
urinary bladder	UBERON:0001255	29.11	gold quality
gall bladder	UBERON:0002110	28.99	silver quality
muscle of leg	UBERON:0001383	28.47	gold quality
duodenum	UBERON:0002114	28.14	gold quality
myometrium	UBERON:0001296	28.08	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting C20orf173, 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-5193	100.00	67.26	1744
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-502-5P	98.77	66.51	906
HSA-MIR-3192-3P	98.62	65.80	970
HSA-MIR-640	98.44	66.93	644
HSA-MIR-3151-3P	97.80	66.16	479
HSA-MIR-1972	97.67	67.38	1172
HSA-MIR-6818-5P	97.50	67.10	1167
HSA-MIR-500B-3P	96.49	65.40	1087

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	st3gal8	ENSDARG00000007494
danio_rerio	st3gal7	ENSDARG00000039064
danio_rerio		ENSDARG00000112644
mus_musculus	6430550D23Rik	ENSMUSG00000074646
rattus_norvegicus	C3h20orf173	ENSRNOG00000047596

Paralogs (14): ST3GAL1 (ENSG00000008513), ST3GAL6 (ENSG00000064225), ST6GALNAC1 (ENSG00000070526), ST6GALNAC2 (ENSG00000070731), ST6GAL1 (ENSG00000073849), ST3GAL4 (ENSG00000110080), ST3GAL5 (ENSG00000115525), ST6GALNAC5 (ENSG00000117069), ST3GAL3 (ENSG00000126091), ST6GALNAC4 (ENSG00000136840), ST6GAL2 (ENSG00000144057), ST3GAL2 (ENSG00000157350), ST6GALNAC6 (ENSG00000160408), ST6GALNAC3 (ENSG00000184005)

Protein

Protein identifiers

Uncharacterized protein C20orf173 — Q96LM9 (reviewed: Q96LM9)

All UniProt accessions (2): Q96LM9, Q4VXR9

Isoforms (2)

UniProt ID	Names	Canonical?
Q96LM9-1	1	yes
Q96LM9-2	2

RefSeq proteins (1): NP_001138822* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038578	GT29-like_sf	Homologous_superfamily
IPR051757	Beta-gal_alpha2-3_sialyltrans	Family

UniProt features (3 total): chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96LM9-F1	47.96	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, ZIC1_01, chr20q11, GOBP_SIALYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, GOBP_GLYCOPROTEIN_BIOSYNTHETIC_PROCESS, GOMF_SIALYLTRANSFERASE_ACTIVITY, HMGA1_TARGET_GENES, MIR1290, MIR6818_5P, MIR3192_3P, MIR6744_5P, MIR3151_3P

GO Biological Process (3): sialylation (GO:0097503), obsolete protein glycosylation (GO:0006486), obsolete ganglioside biosynthetic process via lactosylceramide (GO:0010706)

GO Molecular Function (3): beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836), protein binding (GO:0005515), sialyltransferase activity (GO:0008373)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
macromolecule modification	1
sialyltransferase activity	1
binding	1
glycosyltransferase activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

232 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C20orf173	SPATA31G1	Q5VYM1	608
C20orf173	CABS1	Q96KC9	581
C20orf173	TMCO5A	Q8N6Q1	578
C20orf173	CXorf65	A6NEN9	544
C20orf173	CCDC187	A0A096LP49	541
C20orf173	TMCO2	Q7Z6W1	528
C20orf173	RIMBP3	Q9UFD9	519
C20orf173	CCDC54	Q8NEL0	507
C20orf173	ZC3H11D	Q8NA57	507
C20orf173	FAM209A	Q5JX71	507
C20orf173	LYZL2	Q7Z4W2	507
C20orf173	CFAP184	Q2M329	506
C20orf173	CIMIP4	O43247	506
C20orf173	ROPN1L	Q96C74	479
C20orf173	C22orf23	Q9BZE7	478

IntAct

4 interactions, top by confidence:

A	B	Type	Score
HGS	C20orf173	psi-mi:“MI:0915”(physical association)	0.560
HGS	C20orf173	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): HGS (Two-hybrid), C20orf173 (Negative Genetic)

ESM2 similar proteins: A2APT9, A5PJC7, E1BDF2, O73895, P0C6B2, P0C6B3, P32927, P40238, P51172, Q01114, Q08351, Q0VCS0, Q27969, Q2T9K0, Q3UIW8, Q496M5, Q5F267, Q5FW56, Q5MJ68, Q5R866, Q5R8H1, Q5SZI1, Q5VTJ3, Q5W186, Q68UT4, Q6AZ51, Q6DKI7, Q6IPT2, Q6ISU1, Q6JVE6, Q6PL45, Q6UX52, Q6ZST4, Q70Z44, Q7L513, Q7Z5J1, Q8BH06, Q8K558, Q8NFR9, Q8TCY5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
152798	GRCh38/hg38 20q11.22(chr20:35285724-35744837)x1	Pathogenic

SpliceAI

1049 predictions. Top by Δscore:

Variant	Effect	Δscore
20:35528455:T:C	donor_gain	1.0000
20:35527072:G:C	donor_gain	0.9900
20:35528450:CCTTA:C	donor_gain	0.9900
20:35528454:A:AC	donor_gain	0.9900
20:35528461:A:AC	donor_gain	0.9900
20:35528461:AGAG:A	donor_gain	0.9900
20:35528462:G:C	donor_gain	0.9900
20:35527082:G:C	donor_gain	0.9800
20:35527129:T:TA	donor_gain	0.9800
20:35528448:CACCT:C	donor_loss	0.9800
20:35528449:ACCT:A	donor_loss	0.9800
20:35528450:C:A	donor_loss	0.9800
20:35528452:TTATC:T	donor_gain	0.9800
20:35528786:C:T	acceptor_gain	0.9800
20:35529130:T:TA	donor_gain	0.9800
20:35529557:AC:A	donor_gain	0.9800
20:35529558:CC:C	donor_gain	0.9800
20:35527102:TGTCC:T	donor_gain	0.9700
20:35529068:C:CT	donor_gain	0.9700
20:35529217:T:TA	donor_gain	0.9700
20:35527071:A:AC	donor_gain	0.9600
20:35527115:G:C	donor_gain	0.9600
20:35528453:TATC:T	donor_gain	0.9600
20:35528786:C:CT	acceptor_gain	0.9600
20:35529218:C:A	donor_gain	0.9600
20:35528443:T:TA	donor_gain	0.9500
20:35528545:CT:C	acceptor_loss	0.9500
20:35528546:T:G	acceptor_loss	0.9500
20:35529069:C:CT	donor_gain	0.9500
20:35528545:C:CC	acceptor_gain	0.9400

AlphaMissense

1334 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:35528703:G:C	F109L	0.875
20:35528703:G:T	F109L	0.875
20:35528705:A:G	F109L	0.875
20:35528844:C:A	W62C	0.806
20:35528844:C:G	W62C	0.806
20:35528799:A:C	F77L	0.717
20:35528799:A:T	F77L	0.717
20:35528801:A:G	F77L	0.717
20:35528846:A:G	W62R	0.703
20:35528846:A:T	W62R	0.703
20:35528520:C:A	W118C	0.686
20:35528520:C:G	W118C	0.686
20:35528793:G:C	F79L	0.681
20:35528793:G:T	F79L	0.681
20:35528795:A:G	F79L	0.681
20:35528780:A:G	C84R	0.675
20:35528778:A:C	C84W	0.671
20:35528824:A:G	I69T	0.642
20:35528475:C:A	W133C	0.630
20:35528475:C:G	W133C	0.630
20:35528845:C:G	W62S	0.614
20:35528779:C:T	C84Y	0.613
20:35528787:A:C	C81W	0.606
20:35528283:A:G	I142T	0.567

dbSNP variants (sampled 300 via entrez): RS1000056503 (20:35528118 T>C), RS1000062499 (20:35525850 C>A,T), RS1000665507 (20:35526247 C>G), RS1001014007 (20:35529131 C>A,T), RS1001132696 (20:35527145 C>T), RS1001179914 (20:35527575 T>C), RS1001930367 (20:35527814 C>G), RS1002140284 (20:35527487 G>A,T), RS1002408687 (20:35521766 G>A), RS1002550738 (20:35530538 C>A), RS1002856899 (20:35525646 A>G), RS1002988096 (20:35523743 G>A), RS1003354500 (20:35528938 G>A,C,T), RS1003531470 (20:35522342 T>C), RS1003678076 (20:35520485 A>C)

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

5 associations (top):

Study	Trait	p-value
GCST002337_32	Amyotrophic lateral sclerosis (sporadic)	3.000000e-07
GCST005956_31	Waist-to-hip ratio adjusted for BMI	8.000000e-08
GCST005958_16	Waist-to-hip ratio adjusted for BMI (age >50)	6.000000e-06
GCST005962_40	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	3.000000e-08
GCST010703_112	Brain morphology (MOSTest)	4.000000e-19

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0004346	neuroimaging 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
maleic acid	increases expression	1
Cadmium	decreases expression, increases abundance	1
Phthalic Acids	decreases methylation	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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