SUPT20HL1

Summary

SUPT20HL1 (SUPT20H like 1, HGNC:30773) is a protein-coding gene on chromosome Xp22.11, encoding Transcription factor SPT20 homolog-like 1 (Q3ZLR7).

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of SAGA complex.

Source: NCBI Gene 100130302 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_001136234

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30773
Approved symbol	SUPT20HL1
Name	SUPT20H like 1
Location	Xp22.11
Locus type	gene with protein product
Status	Approved
Aliases	SPT20L
Ensembl gene	ENSG00000223731
Ensembl biotype	protein_coding
Entrez	100130302

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000436466, ENST00000686983

RefSeq mRNA: 1 — MANE Select: NM_001136234 NM_001136234

CCDS: CCDS94581

Canonical transcript exons

ENST00000686983 — 1 exons

Exon	Start	End
ENSE00003932913	24360639	24367839

Expression profiles

Bgee: expression breadth broad, 41 present calls, max score 50.78.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left uterine tube	UBERON:0001303	50.78	gold quality
smooth muscle tissue	UBERON:0001135	50.19	gold quality
body of uterus	UBERON:0009853	49.14	gold quality
myometrium	UBERON:0001296	48.58	gold quality
muscle layer of sigmoid colon	UBERON:0035805	48.20	gold quality
islet of Langerhans	UBERON:0000006	47.88	gold quality
endocervix	UBERON:0000458	46.73	gold quality
uterine cervix	UBERON:0000002	46.44	gold quality
ectocervix	UBERON:0012249	45.84	gold quality
right ovary	UBERON:0002118	45.46	gold quality
fallopian tube	UBERON:0003889	44.81	gold quality
urinary bladder	UBERON:0001255	44.36	silver quality
apex of heart	UBERON:0002098	43.47	silver quality
lower esophagus	UBERON:0013473	42.95	gold quality
lower esophagus muscularis layer	UBERON:0035833	42.95	gold quality
muscle tissue	UBERON:0002385	42.39	gold quality
ovary	UBERON:0000992	42.10	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	42.08	gold quality
gall bladder	UBERON:0002110	41.71	silver quality
vermiform appendix	UBERON:0001154	41.59	silver quality
duodenum	UBERON:0002114	41.50	gold quality
colonic epithelium	UBERON:0000397	41.04	gold quality
colon	UBERON:0001155	40.95	gold quality
skeletal muscle tissue	UBERON:0001134	40.79	gold quality
left ovary	UBERON:0002119	40.46	silver quality
cortical plate	UBERON:0005343	39.98	gold quality
intestine	UBERON:0000160	39.38	gold quality
vagina	UBERON:0000996	39.07	gold quality
hindlimb stylopod muscle	UBERON:0004252	38.62	gold quality
pancreas	UBERON:0001264	38.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.47

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), SUPT20HL2 (ENSG00000223611)

Protein

Protein identifiers

Transcription factor SPT20 homolog-like 1 — Q3ZLR7 (reviewed: Q3ZLR7)

All UniProt accessions (1): A0A7I2YQ69

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPT20 family.

RefSeq proteins (1): NP_001129706* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021950	Spt20	Family
IPR046468	Spt20-like_SEP	Domain

Pfam: PF12090

UniProt features (10 total): region of interest 5, compositionally biased region 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3ZLR7-F1	51.49	0.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (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, GSE13887_ACT_CD4_VS_NO_TREATED_CD4_TCELL_DN, GOCC_HISTONE_ACETYLTRANSFERASE_COMPLEX, GOCC_CHROMATIN, GSE6259_FLT3L_INDUCED_DEC205_POS_DC_VS_CD4_TCELL_DN, GSE6259_DEC205_POS_DC_VS_BCELL_UP

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 (1): SAGA complex (GO:0000124)

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

3 interactions, top by confidence:

A	B	Type	Score
CUL1	LGALS8	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A4GTP4, A7MB40, A8K0R7, B1ASB6, E1BE02, M3WHG5, O18805, P0C7T5, P0C7T6, P0C7V6, P41969, P48382, P70178, P97609, Q3TEI4, Q3UH66, Q3V0C3, Q3ZLR7, Q4R2Z8, Q5SXM2, Q5XHX9, Q61645, Q6P4R8, Q6PDM1, Q6PIJ4, Q6PJG2, Q6U8D7, Q6ZRI6, Q86VY4, Q86Y26, Q8BHP2, Q8K4J6, Q8N196, Q8N1G0, Q91V27, Q91YE5, Q92610, Q96EK2, Q99941, Q99JB6

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

5714 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000626564 (X:24361005 G>A), RS1002755122 (X:24366378 G>A,T), RS1004751561 (X:24367252 G>A,T), RS1005209290 (X:24367640 G>C,T), RS1006760397 (X:24361943 G>A), RS1007721376 (X:24360365 CA>C), RS1008840945 (X:24367970 A>G), RS1009290236 (X:24360437 T>C), RS1009321045 (X:24359789 T>C), RS1009768817 (X:24360951 T>C), RS1011276522 (X:24366257 GAAAGAGTGT>G), RS1011890171 (X:24365744 C>T), RS1012690258 (X:24363757 G>A,T), RS1013280176 (X:24361388 A>G), RS1014239960 (X:24359087 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

5 associations (top):

Study	Trait	p-value
GCST008151_105	Waist circumference	2.000000e-06
GCST008160_107	Waist circumference	2.000000e-06
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

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	1
Phthalic Acids	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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