SUPT20H

Chr 13

SPT20 homolog, SAGA complex component

Also known as: C13, C13orf19, FAM48A, FP757, P38IP, SPT20

NCBI Gene: 55578 ENSG00000102710 UniProt: Q8NEM7

The SUPT20H protein functions as a transcriptional coregulator and is required for MAP kinase p38 activation and autophagy regulation. Mutations cause autosomal recessive developmental delay with dysmorphic features and behavioral abnormalities, typically presenting in early childhood. The gene shows moderate constraint against loss-of-function variants, suggesting some tolerance to reduced protein function.

ResearchSummary from RefSeq, UniProt

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Part of SAGA-type complex. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.81

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.81LOEUF

pLI 0.000

Z-score 2.66

OE 0.60 (0.45–0.81)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.18Z-score

OE missense 0.83 (0.76–0.91)

325 obs / 390.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.60 (0.45–0.81)

0≤0.351.4

Missense OE?0.83 (0.76–0.91)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 30 / 50.3Missense obs/exp: 325 / 390.6Syn Z: 0.65

Background carrier burden — how many people carry a rare variant somewhere in SUPT20H?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 78

998 rare PASS variants

Rare truncating (LoF)

1 in 1,000

177 rare PASS variants

Rare synonymous (reference)

1 in 130

330 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SUPT20H. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 99	1 in 880
South Asian	~43k	1 in 71	1 in 1,000
Remaining (unassigned)	~30k	1 in 61	1 in 900
European (Finnish)	~27k	1 in 320	≈ 1 in 13,000
Admixed American	~22k	1 in 63	1 in 1,400
African / African American	~21k	1 in 68	1 in 1,500
East Asian	~20k	1 in 66	1 in 1,600
Ashkenazi Jewish	~13k	1 in 280	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 82	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 20 of 25 coding exons well covered in gnomAD exomes; exons 5, 12, 15, 16, 18 marginal. Genomes: all 25.? see exons ↓