TFDP3

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

Basic information

Region (hg38): X:133216662-133218354

Links

ENSG00000183434 ∙ NCBI:51270 ∙ OMIM:300772 ∙ HGNC:24603 ∙ Uniprot:Q5H9I0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TFDP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFDP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in TFDP3

This is a list of pathogenic ClinVar variants found in the TFDP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-133217050-C-A		not specified	Uncertain significance (Mar 08, 2025)
X-133217140-G-C		not specified	Uncertain significance (Jan 17, 2024)
X-133217149-C-G		not specified	Uncertain significance (Sep 09, 2024)
X-133217250-A-T		not specified	Uncertain significance (Jan 16, 2025)
X-133217440-C-A		not specified	Uncertain significance (Oct 17, 2024)
X-133217509-C-T		not specified	Uncertain significance (Mar 08, 2024)
X-133217531-G-C		not specified	Uncertain significance (Dec 15, 2023)
X-133217541-T-C		not specified	Uncertain significance (Apr 23, 2024)
X-133217550-T-G		not specified	Uncertain significance (Dec 18, 2023)
X-133217630-T-A		not specified	Uncertain significance (May 31, 2023)
X-133217692-T-C		not specified	Uncertain significance (Jun 28, 2024)
X-133217706-T-C		not specified	Uncertain significance (May 15, 2023)
X-133217737-T-G		not specified	Uncertain significance (Mar 12, 2024)
X-133217773-G-A		not specified	Uncertain significance (Jul 20, 2021)
X-133217819-G-A			Likely benign (Oct 16, 2017)
X-133217841-T-C		not specified	Uncertain significance (May 08, 2024)
X-133217869-G-C		not specified	Uncertain significance (Jan 26, 2022)
X-133217942-C-A		not specified	Uncertain significance (May 14, 2024)
X-133218012-A-G		not specified	Uncertain significance (Sep 17, 2021)
X-133218025-G-T		not specified	Uncertain significance (Mar 05, 2025)
X-133218077-C-A		not specified	Uncertain significance (Jan 04, 2024)
X-133218081-C-A		not specified	Uncertain significance (Jan 22, 2025)
X-133218132-G-A		not specified	Uncertain significance (Feb 15, 2023)
X-133218159-A-G		not specified	Uncertain significance (Jan 07, 2025)
X-133218186-C-A		not specified	Uncertain significance (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFDP3	protein_coding	protein_coding	ENST00000310125	1	1680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0541
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00466

Gene Damage Prediction

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

Gene ontology

• 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
• Cellular component: nucleus;transcription factor complex;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein heterodimerization activity