H2AP

H2A.P histone, the group of H2A histones

Basic information

Region (hg38): X:37990778-37991314

Previous symbols: [ "CXorf27", "HYPM" ]

Links

ENSG00000187516 ∙ NCBI:25763 ∙ ∙ HGNC:18417 ∙ Uniprot:O75409 ∙ 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 H2AP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2AP 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			1	1		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in H2AP

This is a list of pathogenic ClinVar variants found in the H2AP region.

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

Position	Type	Phenotype	Significance	ClinVar
X-37990940-G-A		not specified	Likely benign (Jul 14, 2021)
X-37990963-G-A		not specified	Uncertain significance (Jun 16, 2024)
X-37991075-G-A		not specified	Uncertain significance (Apr 19, 2024)
X-37991111-A-G		not specified	Uncertain significance (Jan 27, 2022)
X-37991159-TTG-T		Short stature	Pathogenic (Nov 18, 2001)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H2AP	protein_coding	protein_coding	ENST00000341016	1	500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.398	60	51.9	1.16	0.00000450	791
Missense in Polyphen		8	6.182	1.2941		108
Synonymous	0.133	18	18.7	0.961	0.00000156	211
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0692

Intolerance Scores

• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.18

Haploinsufficiency Scores

• pHI: 0.0282
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hypm

Gene ontology

• Biological process: chromatin organization
• Cellular component: nuclear chromatin
• Molecular function: DNA binding;protein binding;protein heterodimerization activity