H2AP

protein-coding

H2A.P histone, the group of H2A histones

Gene summary

This gene encodes a protein shown to interact with huntingtin, which contains an expanded polyglutamine tract in individuals with Huntington's disease (PMID: 9700202). [provided by RefSeq, Aug 2011]

Previous symbols:

CXorf27
HYPM

MANE transcript

NM_012274.2

Inheritance

—

ClinVar variants

P:1U:12B:4

Top phenotype

Short stature

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:37,990,779-37,991,314

External References & Databases

Ensembl (ENSG00000187516)

Transcript & Mutation Effects

hg38 • Region Span ~0.5 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 H2AP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 16

Short statureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012274.2. 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						0
missense			12 clinvar	4 clinvar		16
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	1	0	12	4	0	17

Highest pathogenic variant AF is 9.1124724e-7

Loading ClinVar variants...

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_012274.2	RefSeq	NP_036406.1	1	MANE Select
ENST00000341016.5	Ensembl	ENSP00000339511.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chromatin organization

Molecular Function

DNA binding
protein binding
protein heterodimerization activity

Cellular Component

nuclear chromatin

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341016
Coding exons: 1
Length: 500

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

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

Recessive Scores

pRec: 0.0692

Intolerance Scores

RVIS EVS: 0.84
RVIS percentile EVS: 88.18

Essentials

Essential (gene trap): N