TCF19

transcription factor 19, the group of PHD finger proteins

Basic information

Region (hg38): 6:31158330-31167159

Links

ENSG00000137310 ∙ NCBI:6941 ∙ OMIM:600912 ∙ HGNC:11629 ∙ Uniprot:Q9Y242 ∙ 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 TCF19 gene.

• Inborn genetic diseases (13 variants)
• not provided (3 variants)
• Sensorineural hearing loss disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCF19 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			12	2	3	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	3

Variants in TCF19

This is a list of pathogenic ClinVar variants found in the TCF19 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31159539-C-A		not specified	Uncertain significance (Feb 28, 2024)
6-31159539-C-G		not specified	Uncertain significance (Dec 11, 2023)
6-31159597-C-A		not specified	Uncertain significance (Jun 11, 2021)
6-31159663-G-A		not specified	Likely benign (Dec 02, 2021)
6-31159665-G-A		not specified	Uncertain significance (Jan 16, 2024)
6-31159678-G-T		not specified	Uncertain significance (Feb 05, 2024)
6-31161486-G-A		not specified	Uncertain significance (Jul 15, 2021)
6-31161488-C-A		not specified	Uncertain significance (Apr 22, 2022)
6-31161516-C-A		not specified	Uncertain significance (Feb 13, 2023)
6-31161533-C-T			Benign (Apr 30, 2020)
6-31161552-C-T		not specified	Uncertain significance (Feb 17, 2024)
6-31161641-G-A		not specified	Uncertain significance (Jul 12, 2023)
6-31161690-G-A		Sensorineural hearing loss disorder	Uncertain significance (Sep 30, 2020)
6-31161765-G-A			Benign (Jun 26, 2018)
6-31161791-A-C		not specified	Uncertain significance (Feb 28, 2023)
6-31161830-C-T		not specified	Uncertain significance (Sep 14, 2022)
6-31161839-A-G			Benign (Jul 13, 2018)
6-31161870-G-A		not specified	Uncertain significance (Jan 09, 2024)
6-31161962-A-G		not specified	Uncertain significance (Jun 09, 2022)
6-31162497-G-A		not specified	Uncertain significance (Aug 23, 2021)
6-31162520-A-G		not specified	Uncertain significance (Nov 18, 2022)
6-31162544-G-A		not specified	Uncertain significance (Jul 26, 2022)
6-31162622-G-A		not specified	Likely benign (Feb 01, 2023)
6-31162638-C-T		not specified	Uncertain significance (Jan 16, 2024)
6-31164789-C-G		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCF19	protein_coding	protein_coding	ENST00000376257	3	8618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000938	0.820	124700	0	70	124770	0.000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	146	207	0.705	0.0000123	2191
Missense in Polyphen		32	43.269	0.73956		518
Synonymous	1.25	69	83.5	0.827	0.00000464	770
Loss of Function	1.15	6	9.90	0.606	6.34e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000545	0.000535
Ashkenazi Jewish	0.00259	0.00258
East Asian	0.000168	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000219	0.000212
Middle Eastern	0.000168	0.000167
South Asian	0.00	0.00
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential trans-activating factor that could play an important role in the transcription of genes required for the later stages of cell cycle progression.

Intolerance Scores

• loftool: 0.534
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.87

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.204
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.899

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcf19
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell population proliferation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity;protein binding;metal ion binding