HASPIN

protein-coding

histone H3 associated protein kinase

Gene summary

Enables ATP binding activity and histone H3T3 kinase activity. Involved in several processes, including mitotic sister chromatid cohesion; mitotic spindle assembly checkpoint signaling; and protein localization to chromosome, centromeric region. Located in centrosome; nucleoplasm; and spindle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

GSG2

MANE transcript

NM_031965.2

Inheritance

—

ClinVar variants

U:131B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr17:3,723,903-3,726,699

External References & Databases

Ensembl (ENSG00000177602)

Transcript & Mutation Effects

hg38 • Region Span ~2.8 kb

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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 HASPIN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031965.2. 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
missense			130 clinvar	11 clinvar		141
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	131	12	0	143

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031965.2	RefSeq	NP_114171.2	1	MANE Select
ENST00000325418.5	Ensembl	ENSP00000325290.4	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitotic cell cycle
protein phosphorylation
mitotic sister chromatid cohesion
intracellular signal transduction
protein localization to chromosome, centromeric region

Molecular Function

protein kinase activity
protein serine/threonine kinase activity
protein binding
ATP binding
histone kinase activity (H3-T3 specific)

Cellular Component

nucleus
chromosome
cytoplasm
centrosome
spindle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325418
Coding exons: 1
Length: 2857
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.656	412	451	0.913	0.0000235	5171
Missense (PolyPhen)		68	91.568	0.74262		1120
Synonymous	-0.434	191	184	1.04	0.00000955	1658
Loss of Function	1.53	13	20.5	0.635	0.00000106	252

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Serine/threonine-protein kinase that phosphorylates histone H3 at 'Thr-3' (H3T3ph) during mitosis. May act through H3T3ph to both position and modulate activation of AURKB and other components of the chromosomal passenger complex (CPC) at centromeres to ensure proper chromatid cohesion, metaphase alignment and normal progression through the cell cycle. {ECO:0000269|PubMed:11228240, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:17084365, ECO:0000269|PubMed:20705812, ECO:0000269|PubMed:20929775}.;

Recessive Scores

pRec: 0.200

Intolerance Scores

RVIS EVS: 0.16
RVIS percentile EVS: 64.92

Essentials

Essential (gene trap): N