MACROH2A2

macroH2A.2 histone, the group of H2A histones|Macro domain containing

Basic information

Region (hg38): 10:70052544-70112282

Previous symbols: [ "H2AFY2" ]

Links

ENSG00000099284

∙ NCBI:55506 ∙ OMIM:616141 ∙ HGNC:14453 ∙ Uniprot:Q9P0M6 ∙ 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 MACROH2A2 gene.

not_specified (35 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MACROH2A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018649.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			35 clinvar			35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	0	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MACROH2A2	protein_coding	protein_coding	ENST00000373255	8	59485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0236	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.92	110	236	0.466	0.0000151	2408
Missense in Polyphen		25	101.36	0.24664		1044
Synonymous	0.557	100	107	0.932	0.00000809	747
Loss of Function	3.46	1	15.9	0.0629	7.53e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post- translational modifications of histones, also called histone code, and nucleosome remodeling. May be involved in stable X chromosome inactivation. {ECO:0000269|PubMed:15621527}.;
Pathway: Systemic lupus erythematosus - Homo sapiens (human);Necroptosis - Homo sapiens (human);Alcoholism - Homo sapiens (human);Preimplantation Embryo (Consensus)

Recessive Scores

pRec: 0.183

Intolerance Scores

loftool
rvis_EVS: -0.54
rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

pHI: 0.171
hipred: Y
hipred_score: 0.617
ghis: 0.558

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: H2afy2
Phenotype: vision/eye phenotype; immune system phenotype; pigmentation phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name: h2afy2
Affected structure: midbrain hindbrain boundary neural tube
Phenotype tag: abnormal
Phenotype quality: cleft

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;nucleosome assembly;brain development;dosage compensation;positive regulation of keratinocyte differentiation;negative regulation of gene expression, epigenetic;establishment of protein localization to chromatin;negative regulation of transcription of nucleolar large rRNA by RNA polymerase I
Cellular component: nuclear chromosome, telomeric region;nucleosome;nuclear chromatin;Barr body;nucleoplasm;extracellular exosome
Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA binding;chromatin DNA binding;transcription regulatory region DNA binding;protein heterodimerization activity