TFCP2

transcription factor CP2

Basic information

Region (hg38): 12:51093655-51173135

Links

ENSG00000135457 ∙ NCBI:7024 ∙ OMIM:189889 ∙ HGNC:11748 ∙ Uniprot:Q12800 ∙ 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 TFCP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFCP2 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	0	11	0	2

Variants in TFCP2

This is a list of pathogenic ClinVar variants found in the TFCP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-51094453-A-G			Benign (Jan 11, 2019)
12-51095264-T-C		not specified	Uncertain significance (Jan 09, 2024)
12-51098840-G-C		not specified	Uncertain significance (May 24, 2023)
12-51098877-A-T		not specified	Uncertain significance (May 14, 2024)
12-51098903-T-C		not specified	Uncertain significance (Dec 14, 2023)
12-51098907-T-G		not specified	Uncertain significance (Jul 19, 2023)
12-51099772-G-T		not specified	Uncertain significance (Jun 13, 2024)
12-51101963-T-A		not specified	Uncertain significance (Jan 06, 2023)
12-51103696-A-G		not specified	Uncertain significance (Aug 16, 2022)
12-51104166-G-A		not specified	Uncertain significance (Jun 06, 2023)
12-51106557-G-T		not specified	Uncertain significance (Apr 19, 2024)
12-51107285-T-C		not specified	Uncertain significance (Dec 02, 2022)
12-51109174-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-51110869-C-T		TFCP2-related disorder	Likely benign (Oct 28, 2019)
12-51110977-G-A		not specified	Uncertain significance (Aug 08, 2022)
12-51116430-T-A		TFCP2-related disorder	Benign (Apr 16, 2019)
12-51117733-T-C		not specified	Uncertain significance (May 24, 2024)
12-51118732-T-C		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFCP2	protein_coding	protein_coding	ENST00000257915	15	79481

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000358	1.00	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.77	143	272	0.526	0.0000133	3333
Missense in Polyphen		22	72.501	0.30344		892
Synonymous	0.272	95	98.4	0.965	0.00000506	917
Loss of Function	3.04	15	34.2	0.439	0.00000186	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000915	0.0000910
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000136	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds a variety of cellular and viral promoters including fibrinogen, alpha-globin, SV40 and HIV-1 promoters. Activation of the alpha-globin promoter in erythroid cells is via synergistic interaction with UBP1 (By similarity). Functions as part of the SSP (stage selector protein) complex. Facilitates the interaction of the gamma-globin genes with enhancer elements contained in the locus control region in fetal erythroid cells. Interacts by binding to the stage selector element (SSE) in the proximal gamma-globin promoter. {ECO:0000250, ECO:0000269|PubMed:10455131, ECO:0000269|PubMed:1732747, ECO:0000269|PubMed:8035790, ECO:0000269|PubMed:8157699}.
• Pathway: Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

• pRec: 0.247

Intolerance Scores

• loftool: 0.792
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.746
• hipred: Y
• hipred_score: 0.715
• ghis: 0.684

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfcp2
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;mRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytosol;protein-containing complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;sequence-specific DNA binding