TCF19

protein-coding

transcription factor 19, the group of PHD finger proteins

Gene summary

This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

MANE transcript

NM_007109.3

Inheritance

—

ClinVar variants

U:44B:4

Top phenotype

Sensorineural hearing loss disorder

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr6:31,158,331-31,167,159

External References & Databases

Ensembl (ENSG00000137310)

Transcript & Mutation Effects

hg38 • Region Span ~8.8 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 TCF19 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 1

Sensorineural hearing loss disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007109.3. 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						0
missense			44 clinvar	3 clinvar	1 clinvar	48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	3	1	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007109.3	RefSeq	NP_009040.2	3	MANE Select
ENST00000376257.8	Ensembl	ENSP00000365433.3	3	MANE Select
NM_001077511.2	RefSeq	NP_001070979.1	3	Standard
NM_001318908.2	RefSeq	NP_001305837.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
cell population proliferation

Molecular Function

DNA-binding transcription factor activity
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376257
Coding exons: 3
Length: 8618
Individuals with no LoFs: 124700
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 124770
p: 0.000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.51	146	207	0.705	0.0000123	2191
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00013	rare
Latino/Admixed American	0.00041	0.00041	rare
Ashkenazi Jewish	0.0026	0.0026	notable
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.899

Gene Damage Prediction

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