SUB1

protein-coding

SUB1 regulator of transcription

Gene summary

Enables DNA binding activity; identical protein binding activity; and transcription coactivator activity. Involved in RNA polymerase II promoter clearance; negative regulation of DNA metabolic process; and regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of transcription regulator complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_006713.4

Inheritance

—

ClinVar variants

U:7B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr5:32,531,633-32,604,507

External References & Databases

Ensembl (ENSG00000113387)

Transcript & Mutation Effects

hg38 • Region Span ~72.9 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 SUB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 6

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006713.4. 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			1 clinvar	1 clinvar		2
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	7	1	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 77 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006713.4	RefSeq	NP_006704.3	4	MANE Select
ENST00000265073.9	Ensembl	ENSP00000265073.4	4	MANE Select
ENST00000502897.5	Ensembl	ENSP00000427100.1	4	Standard
ENST00000502897.6	Ensembl	ENSP00000427100.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
positive regulation of transcription initiation from RNA polymerase II promoter
SMAD protein signal transduction

Molecular Function

DNA-binding transcription activator activity, RNA polymerase II-specific
single-stranded DNA binding
transcription coactivator activity
RNA binding
protein binding

Cellular Component

nucleus
transcription factor complex
nucleolus
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265073
Coding exons: 4
Length: 72447
Individuals with no LoFs: 124336
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 124338
p: 0.00000804

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.40	33	64.6	0.511	0.00000311	846
Missense (PolyPhen)		6	14.878	0.40327		217
Synonymous	0.510	19	22.0	0.862	0.00000120	217
Loss of Function	2.49	0	7.23	0.00	3.06e-7	94

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA). {ECO:0000269|PubMed:16605275, ECO:0000269|PubMed:16689930, ECO:0000269|PubMed:7628453, ECO:0000269|PubMed:8062391, ECO:0000269|PubMed:8062392, ECO:0000269|PubMed:9360603, ECO:0000269|PubMed:9482861}.;

Recessive Scores

pRec: 0.149

Intolerance Scores

LoFtool: 0.314
RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.993

Gene Damage Prediction

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