PHC2

polyhomeotic homolog 2, the group of Sterile alpha motif domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:33323623-33431095

Previous symbols: [ "EDR2" ]

Links

ENSG00000134686 ∙ NCBI:1912 ∙ OMIM:602979 ∙ HGNC:3183 ∙ Uniprot:Q8IXK0 ∙ 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 PHC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHC2 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			55	1	2	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	56	2	4

Variants in PHC2

This is a list of pathogenic ClinVar variants found in the PHC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-33324871-G-C		not specified	Uncertain significance (Jan 08, 2024)
1-33324933-C-T		not specified	Uncertain significance (May 25, 2022)
1-33328879-A-C		not specified	Uncertain significance (Mar 07, 2024)
1-33328881-C-T		not specified	Uncertain significance (Aug 20, 2024)
1-33328917-G-C		not specified	Uncertain significance (Oct 12, 2022)
1-33328954-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-33328972-T-C		not specified	Uncertain significance (Sep 26, 2023)
1-33328992-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-33329065-T-C		not specified	Uncertain significance (Oct 26, 2022)
1-33329076-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-33330094-G-A		not specified	Uncertain significance (May 31, 2023)
1-33330099-G-A		not specified	Uncertain significance (Mar 13, 2023)
1-33330121-G-C		not specified	Uncertain significance (Oct 20, 2023)
1-33330124-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-33331400-C-A		not specified	Uncertain significance (Aug 06, 2024)
1-33332287-G-A		not specified	Uncertain significance (Aug 19, 2023)
1-33332300-C-T			Benign (Jan 25, 2018)
1-33332385-A-G		not specified	Uncertain significance (Jun 28, 2022)
1-33334091-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-33334206-C-T			Benign (Jun 19, 2018)
1-33334209-T-C		not specified	Uncertain significance (Apr 25, 2023)
1-33334257-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-33334277-A-G		not specified	Uncertain significance (Jan 24, 2023)
1-33334278-T-C		not specified	Uncertain significance (Jan 08, 2024)
1-33354407-C-A		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHC2	protein_coding	protein_coding	ENST00000257118	14	107430

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.546	0.454	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.51	367	529	0.693	0.0000324	5516
Missense in Polyphen		94	164.16	0.57262		1654
Synonymous	1.48	195	223	0.874	0.0000145	1820
Loss of Function	4.45	8	37.3	0.214	0.00000177	401

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000227	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000842	0.0000791
Middle Eastern	0.000227	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility.
• Pathway: miR-targeted genes in adipocytes - TarBase;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;Oxidative Stress Induced Senescence;SUMOylation of DNA damage response and repair proteins;Cellular Senescence;SUMOylation of chromatin organization proteins;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.415
• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.78

Haploinsufficiency Scores

• pHI: 0.686
• hipred: Y
• hipred_score: 0.651
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phc2
• Phenotype: cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; digestive/alimentary phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis
• Cellular component: heterochromatin;nucleus;nucleoplasm;PcG protein complex;PRC1 complex
• Molecular function: DNA binding;protein binding;zinc ion binding;identical protein binding