HASPIN

histone H3 associated protein kinase

Basic information

Region (hg38): 17:3723903-3726699

Previous symbols: [ "GSG2" ]

Links

ENSG00000177602 ∙ NCBI:83903 ∙ OMIM:609240 ∙ HGNC:19682 ∙ Uniprot:Q8TF76 ∙ 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 HASPIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HASPIN 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						0
missense			53	5		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	5	0

Variants in HASPIN

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

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

Position	Type	Phenotype	Significance	ClinVar
17-3723957-C-T		not specified	Uncertain significance (Jun 23, 2023)
17-3723958-C-T		not specified	Uncertain significance (Jun 19, 2024)
17-3723975-C-A		not specified	Uncertain significance (Jul 17, 2024)
17-3723991-C-T		not specified	Uncertain significance (Aug 19, 2023)
17-3724062-T-G		not specified	Uncertain significance (Dec 01, 2022)
17-3724081-G-A		not specified	Uncertain significance (Sep 21, 2023)
17-3724098-G-C		not specified	Uncertain significance (Jun 11, 2024)
17-3724105-C-T		not specified	Uncertain significance (Sep 26, 2024)
17-3724114-C-A		not specified	Uncertain significance (Nov 06, 2023)
17-3724127-C-A		not specified	Uncertain significance (Sep 11, 2024)
17-3724136-C-A		not specified	Uncertain significance (Jan 30, 2024)
17-3724168-G-A		not specified	Likely benign (Aug 13, 2021)
17-3724188-G-A		not specified	Uncertain significance (Aug 20, 2024)
17-3724218-A-G		not specified	Uncertain significance (Aug 02, 2022)
17-3724232-G-T		not specified	Uncertain significance (Dec 12, 2023)
17-3724234-G-C		not specified	Uncertain significance (Feb 27, 2023)
17-3724251-C-T		not specified	Uncertain significance (Mar 29, 2023)
17-3724306-A-G		not specified	Uncertain significance (Mar 06, 2023)
17-3724336-G-C		not specified	Uncertain significance (Aug 02, 2023)
17-3724356-C-G		not specified	Uncertain significance (Nov 09, 2023)
17-3724363-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-3724378-C-G		not specified	Uncertain significance (Apr 24, 2024)
17-3724380-G-C		not specified	Uncertain significance (Jul 13, 2021)
17-3724410-G-A		not specified	Uncertain significance (Jul 07, 2024)
17-3724419-C-G		not specified	Likely benign (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HASPIN	protein_coding	protein_coding	ENST00000325418	1	2857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.99e-7	0.859	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.656	412	451	0.913	0.0000235	5171
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.445
• hipred: Y
• hipred_score: 0.541
• ghis: 0.408

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Haspin
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: mitotic cell cycle;protein phosphorylation;mitotic sister chromatid cohesion;intracellular signal transduction;protein localization to chromosome, centromeric region;histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore
• Cellular component: nucleus;chromosome;cytoplasm;centrosome;spindle
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;histone kinase activity (H3-T3 specific)