TFDP3

protein-coding

transcription factor Dp family member 3, the group of Transcription factor Dp family

Gene summary

This gene encodes a member of the DP family of transcription factors. These factors heterodimerize with E2F proteins to enhance their DNA-binding activity and promote transcription from E2F target genes. This protein functions as a negative regulator and inhibits the DNA binding and transcriptional activities of E2F factors.[provided by RefSeq, May 2010]

MANE transcript

NM_016521.3

Inheritance

—

ClinVar variants

U:36B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:133,216,662-133,218,354

External References & Databases

Ensembl (ENSG00000183434)

Transcript & Mutation Effects

hg38 • Region Span ~1.7 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 TFDP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016521.3. 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
missense			36 clinvar	2 clinvar		38
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	4	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016521.3	RefSeq	NP_057605.3	1	MANE Select
ENST00000310125.5	Ensembl	ENSP00000385461.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G1/S transition of mitotic cell cycle
regulation of transcription by RNA polymerase II
cellular response to DNA damage stimulus
regulation of cell cycle

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein heterodimerization activity

Cellular Component

nucleus
transcription factor complex
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310125
Coding exons: 1
Length: 1680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.150	164	170	0.968	0.0000141	2681
Missense (PolyPhen)		27	28.485	0.94786		490
Synonymous	-1.09	91	78.7	1.16	0.00000776	791
Loss of Function

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	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Competitive inhibitor of E2F-mediated transactivation activity. Impairs E2F-mediated cell-cycle progression from G(1) to S phase. {ECO:0000269|PubMed:16418725, ECO:0000269|PubMed:17062573, ECO:0000269|PubMed:20559320}.;

Recessive Scores

pRec: 0.0569

Intolerance Scores

LoFtool: 0.744
RVIS EVS: 0.73
RVIS percentile EVS: 86.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00466

Gene Damage Prediction

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