SUPT3H

Chr 6

SPT3 homolog, SAGA and STAGA complex component

Also known as: SPT3, SPT3L

NCBI Gene: 8464ENSG00000196284UniProt: O75486

Enables transcription coactivator activity. Involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of SAGA complex and transcription factor TFTC complex. [provided by Alliance of Genome Resources, Jul 2025]

106
ClinVar variants
20
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SUPT3H
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
20 Pathogenic / Likely Pathogenic· 69 VUS of 106 total submissions
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.26LOEUF
pLI 0.000
Z-score 0.65
OE 0.85 (0.59–1.26)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.11Z-score
OE missense 0.98 (0.86–1.11)
169 obs / 173.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.85 (0.59–1.26)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.98 (0.86–1.11)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.94
0≤1.21.6
LoF obs/exp: 18 / 21.2Missense obs/exp: 169 / 173.2Syn Z: 0.37

ClinVar Variant Classifications

106 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic17
Likely Pathogenic3
VUS69
Likely Benign12
Benign4
Conflicting1
17
Pathogenic
3
Likely Pathogenic
69
VUS
12
Likely Benign
4
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
1
15
0
17
Likely Pathogenic
0
0
3
0
3
VUS
0
58
10
1
69
Likely Benign
1
2
8
1
12
Benign
0
0
4
0
4
Conflicting
—1
Total261402106

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

View in ClinVar →

Protein Context — Lollipop Plot

SUPT3H · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genetic variants in the ADAMTS13 and SUPT3H genes are associated with ADAMTS13 activity.
de Vries PS et al.·Blood
2015
Integrative analysis of histone acetyltransferase KAT2A in human cancer.
Li H et al.·Cancer Biomark
2023
EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population.
Li Y et al.·Hum Genet
2019
Patients with isolated oligo/hypodontia caused by RUNX2 duplication.
Molin A et al.·Am J Med Genet A
2015Case report
[Human facial shape related SNP analysis in Han Chinese populations].
Liu M et al.·Yi Chuan
2020
Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis.
Castaño-Betancourt MC et al.·PLoS Genet
2016
Adaptive evolution of loci covarying with the human African Pygmy phenotype.
Mendizabal I et al.·Hum Genet
2012
[Clinical, hormonal and molecular genetic characteristics of 18 cases of disorders of sex development (DSD) 46,XY associated with variants in the SRD5A2 gene].
Kalinchenko NY et al.·Probl Endokrinol (Mosk)
2025Cohort
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools