PHF19

PHD finger protein 19, the group of PHD finger proteins|Tudor domain containing

Basic information

Region (hg38): 9:120855651-120894896

Links

ENSG00000119403

∙ NCBI:26147 ∙ OMIM:609740 ∙ HGNC:24566 ∙ Uniprot:Q5T6S3 ∙ 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 PHF19 gene.

not_specified (42 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015651.3. 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			41 clinvar	1 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF19	protein_coding	protein_coding	ENST00000373896	14	21630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000537	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.35	166	340	0.489	0.0000202	3754
Missense in Polyphen		30	118.42	0.25334		1229
Synonymous	0.981	123	138	0.894	0.00000810	1111
Loss of Function	5.00	3	34.9	0.0859	0.00000190	380

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Probably involved in the transition from an active state to a repressed state in embryonic stem cells: acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting H3K36me3 histone demethylases RIOX1 or KDM2B, leading to demethylation of H3K36 and recruitment of the PRC2 complex that mediates H3K27me3 methylation, followed by de novo silencing. Recruits the PRC2 complex to CpG islands and contributes to embryonic stem cell self-renewal. Also binds dimethylated at 'Lys- 36' (H3K36me2). Isoform 1 and isoform 2 inhibit transcription from an HSV-tk promoter. {ECO:0000269|PubMed:15563832, ECO:0000269|PubMed:21143197, ECO:0000269|PubMed:23104054, ECO:0000269|PubMed:23160351}.;
Pathway: Epigenetic regulation of gene expression;Gene expression (Transcription);PRC2 methylates histones and DNA (Consensus)

Recessive Scores

pRec: 0.123

Intolerance Scores

loftool: 0.154
rvis_EVS: 0.02
rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

pHI: 0.433
hipred: Y
hipred_score: 0.685
ghis: 0.527

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Phf19
Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: chromatin organization;negative regulation of gene expression, epigenetic;positive regulation of transcription, DNA-templated;positive regulation of histone H3-K27 methylation
Cellular component: nucleoplasm;ESC/E(Z) complex
Molecular function: DNA-binding transcription factor activity;protein binding;nucleosome binding;methylated histone binding;sequence-specific DNA binding;metal ion binding