TFCP2

transcription factor CP2

Basic information

Region (hg38): 12:51093656-51173135

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.

not_specified (29 variants)
TFCP2-related_disorder (3 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000005653.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			29 clinvar			29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	0	0

Loading clinvar variants...

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