PHF12

PHD finger protein 12, the group of PHD finger proteins|EMSY complex

Basic information

Region (hg38): 17:28905249-28951771

Links

ENSG00000109118 ∙ NCBI:57649 ∙ OMIM:618645 ∙ HGNC:20816 ∙ Uniprot:Q96QT6 ∙ 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 PHF12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF12 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				1	2	3
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	2	2

Variants in PHF12

This is a list of pathogenic ClinVar variants found in the PHF12 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28906258-C-G		not specified	Uncertain significance (Jul 15, 2021)
17-28906494-C-T		PHF12-related disorder	Uncertain significance (Jun 27, 2023)
17-28906876-G-C		Developmental disorder	Likely benign (Mar 04, 2021)
17-28906947-C-T			Likely benign (Mar 01, 2022)
17-28910119-G-A		PHF12-related disorder	Benign (Apr 29, 2020)
17-28910288-A-G		not specified	Uncertain significance (Aug 28, 2021)
17-28912487-G-A		not specified	Uncertain significance (Oct 04, 2022)
17-28912538-T-C		not specified	Uncertain significance (Jun 21, 2023)
17-28912568-C-T		not specified	Uncertain significance (Sep 14, 2023)
17-28912578-T-C		not specified	Uncertain significance (May 28, 2024)
17-28912612-C-T			Benign (Dec 31, 2018)
17-28912613-G-A		not specified	Uncertain significance (May 14, 2024)
17-28912613-G-C		not specified	Uncertain significance (Jan 31, 2024)
17-28912695-G-T		not specified	Uncertain significance (Oct 29, 2021)
17-28912742-G-A		not specified	Uncertain significance (Nov 21, 2023)
17-28912779-C-T		not specified	Uncertain significance (Apr 26, 2023)
17-28912791-G-C		not specified	Uncertain significance (Mar 08, 2024)
17-28912883-C-T		not specified	Uncertain significance (Feb 28, 2024)
17-28912884-G-A		not specified	Uncertain significance (Nov 13, 2023)
17-28912913-T-C		not specified	Uncertain significance (Aug 03, 2022)
17-28912961-G-A		not specified	Uncertain significance (Jun 29, 2022)
17-28913037-G-T		not specified	Uncertain significance (Jun 29, 2023)
17-28913050-G-C		not specified	Uncertain significance (Feb 16, 2023)
17-28913141-G-A		not specified	Uncertain significance (Jan 08, 2024)
17-28913240-A-G		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF12	protein_coding	protein_coding	ENST00000332830	15	46522

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000122	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	439	607	0.723	0.0000354	6561
Missense in Polyphen		59	139.26	0.42367		1468
Synonymous	2.08	211	253	0.833	0.0000161	2048
Loss of Function	6.07	2	46.8	0.0428	0.00000264	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. Involved in recruitment of functional SIN3A complexes to DNA. Represses transcription at least in part through the activity of an associated histone deacetylase (HDAC). May also repress transcription in a SIN3A-independent manner through recruitment of functional AES complexes to DNA. {ECO:0000269|PubMed:11390640, ECO:0000303|PubMed:11390640}.

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.0335
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.52

Haploinsufficiency Scores

• pHI: 0.764
• hipred: Y
• hipred_score: 0.794
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf12

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;Sin3 complex;transcriptional repressor complex;Sin3-type complex
• Molecular function: transcription corepressor binding;transcription corepressor activity;protein binding;phosphatidylinositol binding;metal ion binding