PHF1

PHD finger protein 1, the group of PHD finger proteins|Tudor domain containing

Basic information

Region (hg38): 6:33410399-33416453

Links

ENSG00000112511 ∙ NCBI:5252 ∙ OMIM:602881 ∙ HGNC:8919 ∙ Uniprot:O43189 ∙ 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 PHF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF1 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			27	3		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	3	0

Variants in PHF1

This is a list of pathogenic ClinVar variants found in the PHF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-33412269-G-A		not specified	Likely benign (Feb 12, 2025)
6-33412282-C-A		not specified	Uncertain significance (Jan 21, 2025)
6-33412288-C-G		not specified	Uncertain significance (Aug 28, 2021)
6-33412295-G-T		not specified	Uncertain significance (Sep 30, 2024)
6-33412315-C-T		not specified	Uncertain significance (Jan 10, 2025)
6-33412354-C-T		not specified	Uncertain significance (Dec 14, 2021)
6-33412411-A-G		not specified	Uncertain significance (Mar 07, 2025)
6-33412703-C-G		not specified	Uncertain significance (Feb 07, 2025)
6-33412748-G-A		not specified	Uncertain significance (Jan 08, 2024)
6-33412763-C-T		not specified	Uncertain significance (Oct 26, 2022)
6-33412787-C-T		not specified	Uncertain significance (May 24, 2024)
6-33412788-G-A		not specified	Uncertain significance (May 11, 2022)
6-33413532-T-C			Uncertain significance (Apr 06, 2023)
6-33413761-C-T		not specified	Uncertain significance (Sep 28, 2021)
6-33414072-G-A		not specified	Uncertain significance (Aug 14, 2023)
6-33414091-G-A		not specified	Uncertain significance (Nov 12, 2024)
6-33414332-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-33414361-G-A		not specified	Uncertain significance (Jun 10, 2024)
6-33414793-C-T		not specified	Uncertain significance (Sep 02, 2024)
6-33414992-C-T		not specified	Uncertain significance (Jan 26, 2023)
6-33415011-G-A		not specified	Uncertain significance (Nov 12, 2024)
6-33415017-C-T		not specified	Uncertain significance (Jan 22, 2024)
6-33415040-A-C		not specified	Likely benign (Jul 30, 2024)
6-33415077-C-T		not specified	Uncertain significance (Jul 20, 2021)
6-33415085-C-T		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF1	protein_coding	protein_coding	ENST00000374516	14	6055

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000441	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	248	341	0.726	0.0000202	3608
Missense in Polyphen		32	97.53	0.3281		1074
Synonymous	0.0836	122	123	0.990	0.00000607	1209
Loss of Function	4.83	2	31.0	0.0645	0.00000158	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Involved in DNA damage response and is recruited at double-strand breaks (DSBs). Acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting the PRC2 complex: it is however unclear whether recruitment of the PRC2 complex to H3K36me3 leads to enhance or inhibit H3K27me3 methylation mediated by the PRC2 complex. According to some reports, PRC2 recruitment by PHF1 promotes H3K27me3 and subsequent gene silencing by inducing spreading of PRC2 and H3K27me3 into H3K36me3 loci (PubMed:18285464 and PubMed:23273982). According to another report, PHF1 recruits the PRC2 complex at double-strand breaks (DSBs) and inhibits the activity of PRC2 (PubMed:23142980). Regulates p53/TP53 stability and prolonges its turnover: may act by specifically binding to a methylated from of p53/TP53. {ECO:0000269|PubMed:18086877, ECO:0000269|PubMed:18285464, ECO:0000269|PubMed:18385154, ECO:0000269|PubMed:23142980, ECO:0000269|PubMed:23150668, ECO:0000269|PubMed:23273982}.
• Disease: DISEASE: Note=A chromosomal aberration involving PHF1 may be a cause of endometrial stromal tumors. Translocation t(6;7)(p21;p22) with JAZF1. Translocation t(1;6)(p34;p21) with MEAF6. {ECO:0000269|PubMed:16397222, ECO:0000269|PubMed:22761769}.
• Pathway: Epigenetic regulation of gene expression;Gene expression (Transcription);PRC2 methylates histones and DNA (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.252
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.662
• hipred: Y
• hipred_score: 0.675
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf1

Gene ontology

• Biological process: chromatin organization;cellular response to DNA damage stimulus;negative regulation of gene expression, epigenetic;positive regulation of transcription, DNA-templated;negative regulation of histone H3-K27 methylation;positive regulation of histone H3-K27 methylation
• Cellular component: nucleus;nucleoplasm;cytoplasm;centrosome;ESC/E(Z) complex;site of double-strand break
• Molecular function: DNA-binding transcription factor activity;protein binding;nucleosome binding;methylated histone binding;sequence-specific DNA binding;metal ion binding