SUPT20HL2

Summary

SUPT20HL2 (SUPT20H like 2, HGNC:31797) is a protein-coding gene on chromosome Xp22.11, encoding Transcription factor SPT20 homolog-like 2 (P0C7V6).

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in extracellular space.

Source: NCBI Gene 170067 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001136233

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31797
Approved symbol	SUPT20HL2
Name	SUPT20H like 2
Location	Xp22.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000223611
Ensembl biotype	protein_coding
Entrez	170067

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000486479

RefSeq mRNA: 1 — MANE Select: NM_001136233 NM_001136233

CCDS: CCDS94580

Canonical transcript exons

ENST00000486479 — 1 exons

Exon	Start	End
ENSE00001879591	24308210	24314069

Expression profiles

Bgee: expression breadth broad, 26 present calls, max score 78.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0047 / max 4.9619, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
209634	0.0047	3

Top tissues by expression

114 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	78.24	gold quality
left uterine tube	UBERON:0001303	51.25	gold quality
smooth muscle tissue	UBERON:0001135	50.11	gold quality
colonic epithelium	UBERON:0000397	49.66	gold quality
fallopian tube	UBERON:0003889	47.77	gold quality
myometrium	UBERON:0001296	45.11	gold quality
vermiform appendix	UBERON:0001154	44.92	silver quality
body of uterus	UBERON:0009853	44.45	gold quality
islet of Langerhans	UBERON:0000006	43.49	gold quality
gall bladder	UBERON:0002110	42.24	silver quality
right ovary	UBERON:0002118	41.73	gold quality
uterine cervix	UBERON:0000002	39.54	silver quality
muscle layer of sigmoid colon	UBERON:0035805	39.54	silver quality
stromal cell of endometrium	CL:0002255	39.22	gold quality
muscle tissue	UBERON:0002385	39.14	gold quality
endocervix	UBERON:0000458	38.53	gold quality
bone marrow cell	CL:0002092	38.04	gold quality
ovary	UBERON:0000992	38.01	gold quality
ganglionic eminence	UBERON:0004023	37.16	gold quality
testis	UBERON:0000473	37.08	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
skeletal muscle tissue	UBERON:0001134	36.39	gold quality
ectocervix	UBERON:0012249	36.19	gold quality
right testis	UBERON:0004534	36.02	gold quality
placenta	UBERON:0001987	35.82	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.39	gold quality
sural nerve	UBERON:0015488	35.32	gold quality
colon	UBERON:0001155	34.64	silver quality
left testis	UBERON:0004533	34.32	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-97	yes	232.46
E-MTAB-6379	no	57.37
E-GEOD-70580	no	56.28
E-ENAD-27	no	4.36
E-ANND-3	no	0.98

Regulation

Is transcription factor: no

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	supt20	ENSDARG00000078658
mus_musculus	Gm61616	ENSMUSG00000121951
mus_musculus	Gm61617	ENSMUSG00000121952
rattus_norvegicus	Supt20hl1	ENSRNOG00000042530
rattus_norvegicus	Supt20hl2	ENSRNOG00000048066
drosophila_melanogaster	Spt20	FBGN0036374

Paralogs (2): SUPT20H (ENSG00000102710), SUPT20HL1 (ENSG00000223731)

Protein

Protein identifiers

Transcription factor SPT20 homolog-like 2 — P0C7V6 (reviewed: P0C7V6)

All UniProt accessions (1): P0C7V6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPT20 family.

RefSeq proteins (1): NP_001129705* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021950	Spt20	Family
IPR046468	Spt20-like_SEP	Domain

Pfam: PF12090

UniProt features (12 total): compositionally biased region 6, region of interest 5, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7V6-F1	51.14	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): GOCC_SAGA_COMPLEX, GOCC_TRANSFERASE_COMPLEX, GOCC_SAGA_TYPE_COMPLEX, chrXp22, GOCC_PEPTIDASE_COMPLEX, GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GOMF_MOLECULAR_ADAPTOR_ACTIVITY, GOCC_INTRACELLULAR_PROTEIN_CONTAINING_COMPLEX, GOCC_ACETYLTRANSFERASE_COMPLEX, GOCC_HISTONE_ACETYLTRANSFERASE_COMPLEX, GOCC_CHROMATIN

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (1): transcription coregulator activity (GO:0003712)

GO Cellular Component (2): SAGA complex (GO:0000124), obsolete extracellular space (GO:0005615)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
transcription regulator activity	1
SAGA-type complex	1
DUBm complex	1
peptidase complex	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6NNL0, A8K0R7, B1AL46, B1ASB6, C9JSJ3, O54824, O88286, P0C7V6, P97303, Q05AH6, Q14005, Q2YDE2, Q32LE6, Q3TEI4, Q3TQ03, Q3V0C3, Q497V6, Q498S6, Q4R2Z8, Q5PQK4, Q5R8C5, Q5RCQ2, Q5VT03, Q66JV7, Q68DK7, Q69ZB8, Q6P1D7, Q6PDM1, Q6PG95, Q6ZMY3, Q6ZRI6, Q76N32, Q7TN08, Q7Z4V0, Q80XI1, Q86Y26, Q8BHP2, Q8BP99, Q8BZW2, Q8CBC4

Diamond homologs: P0C7V6, Q3ZLR7, Q5R724, Q5ZM71, Q66HC7, Q7TT00, Q8NEM7, F4IDB2

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	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000174091 (X:24315512 T>G), RS1000478291 (X:24314291 TA>T), RS1001486927 (X:24311960 T>C,G), RS1002457144 (X:24310698 C>T), RS1002900032 (X:24310368 G>A), RS1003850802 (X:24307936 T>C), RS1004300572 (X:24310859 G>C), RS1005304422 (X:24308000 C>T), RS1005440308 (X:24308462 T>C), RS1006274329 (X:24316002 T>A), RS1007416827 (X:24313431 C>T), RS1008007879 (X:24311702 A>G,T), RS1008268490 (X:24311387 C>A,T), RS1008963320 (X:24310254 G>A,T), RS1009408911 (X:24309907 T>A)

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
GCST010725_25	Malaria	7.000000e-06
GCST010725_41	Malaria	8.000000e-06
GCST010725_82	Malaria	8.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
manganese chloride	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Manganese	decreases expression, increases abundance	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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