SUPT20HL1

Chr X

SUPT20H like 1

Also known as: FAM48B1, SPT20L

NCBI Gene: 100130302 ENSG00000223731 UniProt: Q3ZLR7

The SUPT20HL1 protein is predicted to function as a transcription coregulator and component of the SAGA complex, regulating RNA polymerase II-mediated transcription. Currently, no specific diseases have been definitively associated with mutations in this gene in established clinical databases. The clinical significance of variants in SUPT20HL1 remains to be determined.

ResearchSummary from RefSeq

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. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

LOFmechanism

Clinical Summary— SUPT20HL1

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ClinVar Variants

2 VUS of 12 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

This gene — mechanism propensity

0.3693th %ile

GOF

0.3887th %ile

LOF

0.68top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

12 submitted variants in ClinVar

ClinVar

Classification Summary

VUS2

Likely Benign10

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	2	0	2
Likely Benign	4	6	10
Benign	0	0	0
Total	6	6	12

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

80 pathogenic / likely-pathogenic (of 88) ClinVar copy-number / structural variants overlap SUPT20HL1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →