HP1BP3

heterochromatin protein 1 binding protein 3

Basic information

Region (hg38): 1:20740266-20787323

Links

ENSG00000127483 ∙ NCBI:50809 ∙ OMIM:616072 ∙ HGNC:24973 ∙ Uniprot:Q5SSJ5 ∙ 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 HP1BP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HP1BP3 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	26	1	1

Variants in HP1BP3

This is a list of pathogenic ClinVar variants found in the HP1BP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20744835-T-G		not specified	Uncertain significance (Mar 01, 2023)
1-20744847-G-T		not specified	Uncertain significance (Dec 11, 2024)
1-20744866-T-C			Benign (May 16, 2018)
1-20744936-T-G		not specified	Uncertain significance (Dec 13, 2023)
1-20744963-G-A		not specified	Uncertain significance (Sep 02, 2024)
1-20745051-C-T		not specified	Likely benign (Nov 09, 2022)
1-20745056-T-C		not specified	Uncertain significance (Jan 04, 2025)
1-20745062-G-A		not specified	Uncertain significance (Oct 18, 2021)
1-20745550-T-C		not specified	Uncertain significance (Feb 07, 2025)
1-20745579-T-C		not specified	Uncertain significance (Jun 30, 2023)
1-20745616-T-C		not specified	Uncertain significance (Dec 04, 2023)
1-20745619-A-G		not specified	Uncertain significance (Aug 20, 2024)
1-20745632-T-G		not specified	Uncertain significance (Dec 19, 2023)
1-20745633-T-C		not specified	Uncertain significance (Dec 19, 2023)
1-20747623-C-T		not specified	Uncertain significance (Dec 20, 2024)
1-20749840-T-G		not specified	Uncertain significance (Nov 21, 2022)
1-20749855-G-A		not specified	Uncertain significance (Oct 14, 2023)
1-20749860-G-A		not specified	Uncertain significance (Dec 27, 2022)
1-20757210-G-C		not specified	Uncertain significance (Jul 26, 2021)
1-20757237-C-G		not specified	Uncertain significance (Oct 28, 2024)
1-20757237-C-T		not specified	Uncertain significance (Jul 12, 2022)
1-20765474-G-C		not specified	Uncertain significance (Mar 11, 2025)
1-20773506-G-A		not specified	Uncertain significance (Jun 30, 2024)
1-20776613-C-T		not specified	Uncertain significance (Dec 31, 2023)
1-20776636-T-C		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HP1BP3	protein_coding	protein_coding	ENST00000312239	12	44663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0158	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	186	293	0.636	0.0000149	3587
Missense in Polyphen		51	116.54	0.43761		1462
Synonymous	-1.04	125	111	1.13	0.00000617	1075
Loss of Function	4.16	3	25.8	0.116	0.00000115	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000619	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of heterochromatin that maintains heterochromatin integrity during G1/S progression and regulates the duration of G1 phase to critically influence cell proliferative capacity (PubMed:24830416). Mediates chromatin condensation during hypoxia, leading to increased tumor cell viability, radio-resistance, chemo-resistance and self- renewal(PubMed:25100860). {ECO:0000269|PubMed:24830416, ECO:0000269|PubMed:25100860}.

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.260
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.520
• hipred: Y
• hipred_score: 0.673
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hp1bp3
• Phenotype: growth/size/body region 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)

Gene ontology

• Biological process: nucleosome assembly;regulation of transcription, DNA-templated;regulation of cell population proliferation;heterochromatin organization;cellular response to hypoxia;regulation of nucleus size
• Cellular component: nucleosome;nucleus;chromosome;nuclear speck
• Molecular function: DNA binding;protein binding;nucleosome binding