HP1BP3

protein-coding

heterochromatin protein 1 binding protein 3

Gene summary

Enables DNA binding activity and nucleosome binding activity. Involved in several processes, including cellular response to hypoxia; heterochromatin organization; and regulation of nucleus size. Located in chromosome and nuclear speck. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001372052.1

Inheritance

—

ClinVar variants

U:58B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr1:20,740,266-20,787,323

External References & Databases

Ensembl (ENSG00000127483)

Transcript & Mutation Effects

hg38 • Region Span ~47.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HP1BP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001372052.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			50 clinvar	2 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	58	2	1	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001372052.1	RefSeq	NP_001358981.1	12	MANE Select
ENST00000438032.6	Ensembl	ENSP00000403039.2	12	MANE Select
NM_001376787.1	RefSeq	NP_001363716.1	12	Standard
NM_001376788.1	RefSeq	NP_001363717.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nucleosome assembly
regulation of transcription, DNA-templated
regulation of cell population proliferation
heterochromatin organization
cellular response to hypoxia

Molecular Function

DNA binding
protein binding
nucleosome binding

Cellular Component

nucleosome
nucleus
chromosome
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000312239
Coding exons: 12
Length: 44663
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125747
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.21	186	293	0.636	0.0000149	3587
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.926

Gene Damage Prediction

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