DMAP1

DNA methyltransferase 1 associated protein 1, the group of Myb/SANT domain containing|SRCAP complex|Tip60/Nua4 histone acetyltransferase complex subunits

Basic information

Region (hg38): 1:44213455-44220681

Links

ENSG00000178028 ∙ NCBI:55929 ∙ OMIM:605077 ∙ HGNC:18291 ∙ Uniprot:Q9NPF5 ∙ 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 DMAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMAP1 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			25			25
nonsense			1			1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	1	27	0	0

Variants in DMAP1

This is a list of pathogenic ClinVar variants found in the DMAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-44213757-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-44213775-C-T		not specified	Uncertain significance (Dec 10, 2024)
1-44214366-C-A		not specified	Uncertain significance (Sep 12, 2023)
1-44214747-G-A		not specified	Uncertain significance (Apr 11, 2023)
1-44214762-A-G		not specified	Uncertain significance (Aug 11, 2024)
1-44214783-G-A		not specified	Uncertain significance (Jan 06, 2023)
1-44214796-G-C		Intellectual disability;Abnormal facial shape;Seizure	Uncertain significance (Aug 01, 2021)
1-44214894-A-G		not specified	Uncertain significance (Dec 11, 2023)
1-44218310-G-C			Uncertain significance (Jul 29, 2022)
1-44218356-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-44218359-C-T		not specified	Uncertain significance (Sep 22, 2022)
1-44218428-T-C		Profound global developmental delay;Generalized hypotonia	Uncertain significance (Apr 29, 2021)
1-44218432-T-C		not specified	Uncertain significance (Sep 25, 2024)
1-44218438-T-C		not specified	Uncertain significance (May 14, 2024)
1-44218444-A-G		not specified	Uncertain significance (Feb 12, 2025)
1-44218457-C-A		not specified	Uncertain significance (Dec 02, 2022)
1-44218616-G-A		DMAP1-associated disorder	Uncertain significance (Dec 02, 2022)
1-44218622-A-C		not specified	Uncertain significance (Jun 24, 2022)
1-44218628-T-C		not specified	Uncertain significance (Feb 13, 2025)
1-44218705-C-T		DMAP1-associated disorder	Uncertain significance (Dec 02, 2022)
1-44218726-G-C		not specified	Uncertain significance (Dec 07, 2021)
1-44218730-G-A		not specified	Uncertain significance (Dec 06, 2023)
1-44219056-G-A		not specified	Uncertain significance (Sep 03, 2024)
1-44219165-C-G		not specified	Uncertain significance (Oct 22, 2024)
1-44219183-G-A		not specified	Uncertain significance (Jul 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMAP1	protein_coding	protein_coding	ENST00000372289	10	7227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0411	0.959	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	186	297	0.626	0.0000199	2994
Missense in Polyphen		61	109.68	0.55614		999
Synonymous	-0.0533	117	116	1.01	0.00000706	961
Loss of Function	3.22	7	24.0	0.292	0.00000137	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000284	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.000284	0.000272
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transcription repression and activation. Its interaction with HDAC2 may provide a mechanism for histone deacetylation in heterochromatin following replication of DNA at late firing origins. Can also repress transcription independently of histone deacetylase activity. May specifically potentiate DAXX- mediated repression of glucocorticoid receptor-dependent transcription. Component of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones 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. This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senescence, apoptosis, and DNA repair. NuA4 may also play a direct role in DNA repair when recruited to sites of DNA damage. Participates in the nuclear localization of URI1 and increases its transcriptional corepressor activity. {ECO:0000269|PubMed:14665632, ECO:0000269|PubMed:14966270, ECO:0000269|PubMed:14978102, ECO:0000269|PubMed:15367675}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.0778
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.212
• hipred: Y
• hipred_score: 0.745
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dmap1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; 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)

Zebrafish Information Network

• Gene name: dmap1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;DNA repair;DNA methylation;chromatin remodeling;regulation of growth;positive regulation of protein import into nucleus;histone H4 acetylation;histone H2A acetylation;response to ethanol;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;replication fork;cytoplasm;cytosol;NuA4 histone acetyltransferase complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II repressing transcription factor binding;transcription corepressor activity;protein binding