PHC3

polyhomeotic homolog 3, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 3:170086732-170181749

Links

ENSG00000173889 ∙ NCBI:80012 ∙ OMIM:620031 ∙ HGNC:15682 ∙ Uniprot:Q8NDX5 ∙ 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 PHC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHC3 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		1
missense			56			56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	1	0

Variants in PHC3

This is a list of pathogenic ClinVar variants found in the PHC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-170097246-G-A		not specified	Uncertain significance (Mar 07, 2024)
3-170097341-A-G			Likely benign (Apr 01, 2023)
3-170102577-C-T		not specified	Uncertain significance (Apr 15, 2024)
3-170102593-G-A		not specified	Uncertain significance (May 12, 2024)
3-170102601-C-T		not specified	Uncertain significance (Feb 21, 2024)
3-170102602-G-A		not specified	Uncertain significance (Apr 19, 2023)
3-170102604-T-C		not specified	Uncertain significance (Nov 14, 2024)
3-170102629-G-A		not specified	Uncertain significance (Apr 09, 2024)
3-170102635-G-A		not specified	Uncertain significance (Feb 06, 2024)
3-170102668-G-A		not specified	Uncertain significance (Aug 19, 2023)
3-170102692-A-G		not specified	Uncertain significance (Jan 21, 2025)
3-170102824-G-A		not specified	Uncertain significance (Dec 15, 2023)
3-170102851-C-T		not specified	Uncertain significance (Sep 03, 2024)
3-170102857-C-T		not specified	Uncertain significance (Aug 14, 2023)
3-170102882-G-A		not specified	Uncertain significance (Jun 29, 2022)
3-170102907-A-C		not specified	Uncertain significance (Oct 12, 2022)
3-170106944-T-C		not specified	Uncertain significance (Mar 29, 2023)
3-170113381-T-C		not specified	Uncertain significance (Sep 08, 2024)
3-170113443-A-G		not specified	Uncertain significance (Mar 03, 2025)
3-170113453-T-C		not specified	Uncertain significance (Dec 27, 2023)
3-170117290-T-G		not specified	Uncertain significance (Feb 16, 2023)
3-170117297-T-C		not specified	Uncertain significance (Nov 08, 2024)
3-170117336-T-A		not specified	Uncertain significance (May 31, 2023)
3-170117342-T-C		not specified	Uncertain significance (Jan 08, 2024)
3-170117344-G-C		not specified	Uncertain significance (Aug 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHC3	protein_coding	protein_coding	ENST00000495893	15	95018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.78e-8	124581	0	3	124584	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	425	537	0.791	0.0000282	6436
Missense in Polyphen		189	273.09	0.69208		3317
Synonymous	-1.55	217	190	1.14	0.00000940	2048
Loss of Function	6.36	1	49.1	0.0204	0.00000263	532

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000557
Finnish	0.00	0.00
European (Non-Finnish)	0.00000888	0.00000885
Middle Eastern	0.0000558	0.0000557
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. {ECO:0000269|PubMed:12167701}.
• Pathway: Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Transcriptional Regulation by E2F6;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: 0.150

Intolerance Scores

• loftool: 0.227
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.63

Haploinsufficiency Scores

• pHI: 0.797
• hipred: Y
• hipred_score: 0.580
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phc3

Gene ontology

• Biological process: multicellular organism development;negative regulation of G0 to G1 transition
• Cellular component: nucleus;nucleoplasm;PcG protein complex;PRC1 complex
• Molecular function: DNA binding;protein binding;zinc ion binding