SUPT3H

protein-coding

SPT3 homolog, SAGA and STAGA complex component, the group of MicroRNA protein coding host genes|SAGA complex

Gene summary

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]

MANE transcript

NM_003599.4

Inheritance

—

ClinVar variants

U:50B:1

Top phenotype

Cleidocranial dysostosis

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr6:44,809,317-45,377,953

External References & Databases

Ensembl (ENSG00000196284)

Transcript & Mutation Effects

hg38 • Region Span ~568.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SUPT3H variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 16

Cleidocranial dysostosisTotal: 6

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003599.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	50	1	0	51

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003599.4	RefSeq	NP_003590.1	10	MANE Select
ENST00000371459.6	Ensembl	ENSP00000360514.1	10	MANE Select
NM_001261823.2	RefSeq	NP_001248752.1	6	Standard
NM_001350324.2	RefSeq	NP_001337253.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transcriptional misregulation in cancer - Homo sapiens (human)
Chromatin modifying enzymes
HATs acetylate histones
Chromatin organization
C-MYC pathway

Biological Process

regulation of transcription, DNA-templated
regulation of transcription by RNA polymerase II
transcription by RNA polymerase II
histone deubiquitination
histone H3 acetylation

Molecular Function

DNA binding
transcription coregulator activity
transcription coactivator activity
histone acetyltransferase activity
protein heterodimerization activity

Cellular Component

nucleus
nucleoplasm
transcription factor TFIID complex
STAGA complex
transcription factor TFTC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371460
Coding exons: 11
Length: 568637
Individuals with no LoFs: 125413
Homozygous LoFs: 1
Heterozygous LoFs: 334
Defined: 125748
p: 0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.115	169	173	0.976	0.00000889	2175
Missense (PolyPhen)		44	51.455	0.85512		622
Synonymous	0.373	54	57.6	0.938	0.00000301	589
Loss of Function	0.647	18	21.2	0.849	0.00000123	242

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.0027	0.0026	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00016	0.00016	rare
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.0013	0.0013	notable
South Asian	0.0016	0.0016	notable
Other	0.0024	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable transcriptional activator. {ECO:0000269|PubMed:9787080}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.909
RVIS EVS: 1.22
RVIS percentile EVS: 93.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.0618

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium