MEAF6

MYST/Esa1 associated factor 6, the group of Tip60/Nua4 histone acetyltransferase complex subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:37489993-37514766

Previous symbols: [ "C1orf149" ]

Links

ENSG00000163875

∙ NCBI:64769 ∙ OMIM:611001 ∙ HGNC:25674 ∙ Uniprot:Q9HAF1 ∙ 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 MEAF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEAF6 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			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in MEAF6

This is a list of pathogenic ClinVar variants found in the MEAF6 region.

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

Position	Phenotype	Significance	ClinVar
1-37496708-C-T	not specified	Uncertain significance (Jul 30, 2024)	3394215
1-37501825-C-T	not specified	Uncertain significance (Nov 30, 2021)	2262794
1-37501927-T-C	not specified	Uncertain significance (Jun 27, 2022)	2297936
1-37501967-T-G	not specified	Uncertain significance (Nov 13, 2024)	3394217
1-37509477-T-C	not specified	Uncertain significance (Dec 27, 2023)	3124777
1-37509537-G-C	not specified	Uncertain significance (Sep 12, 2023)	2622519
1-37514722-G-A	not specified	Uncertain significance (Apr 23, 2024)	3293915
1-37514740-T-C	not specified	Uncertain significance (Feb 16, 2023)	2467374
1-37514742-G-A	not specified	Uncertain significance (Jan 02, 2024)	3124779

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEAF6	protein_coding	protein_coding	ENST00000373075	8	22200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.128	0.868	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	44	110	0.401	0.00000604	1314
Missense in Polyphen		18	48.078	0.37439		595
Synonymous	0.381	37	40.1	0.923	0.00000194	360
Loss of Function	2.49	4	14.1	0.284	8.25e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histone H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. Component of the HBO1 complex which has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo. Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. {ECO:0000269|PubMed:14966270, ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:18794358}.;
Disease: DISEASE: Note=A chromosomal aberration involving MEAF6 may be a cause of endometrial stromal tumors. Translocation t(1;6)(p34;p21) with PHF1. {ECO:0000269|PubMed:22761769}.;
Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

pRec: 0.103

Intolerance Scores

loftool: 0.334
rvis_EVS: -0.1
rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

pHI: 0.185
hipred: Y
hipred_score: 0.859
ghis: 0.639

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Meaf6
Phenotype

Gene ontology

Biological process: histone H2A acetylation;histone H3-K23 acetylation;histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K12 acetylation;histone H4-K16 acetylation;histone H3-K14 acetylation;regulation of signal transduction by p53 class mediator
Cellular component: kinetochore;condensed chromosome kinetochore;nucleoplasm;nucleolus;NuA4 histone acetyltransferase complex;MOZ/MORF histone acetyltransferase complex;NuA3a histone acetyltransferase complex;NuA3b histone acetyltransferase complex
Molecular function: protein binding;histone acetyltransferase activity (H3-K23 specific)