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): 1:44213454-44220681
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 17 | 17 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 1 | 19 | 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) | ||
| 1-44214366-C-A | not specified | Uncertain significance (Sep 12, 2023) | ||
| 1-44214747-G-A | not specified | Uncertain significance (Apr 11, 2023) | ||
| 1-44214783-G-A | not specified | Uncertain significance (Jan 06, 2023) | ||
| 1-44214796-G-C | Intellectual disability;Seizure;Abnormal facial shape | 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) | ||
| 1-44218438-T-C | not specified | Uncertain significance (May 14, 2024) | ||
| 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) | ||
| 1-44218705-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) | ||
| 1-44219183-G-A | not specified | Uncertain significance (May 04, 2022) | ||
| 1-44219849-TG-T | Intellectual disability;Seizure;Abnormal facial shape | Likely pathogenic (Aug 01, 2021) | ||
| 1-44220149-A-T | not specified | Uncertain significance (Sep 21, 2023) | ||
| 1-44220172-G-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 1-44220312-A-G | Uncertain significance (Jul 29, 2022) | |||
| 1-44220595-G-A | not specified | Uncertain significance (Jan 06, 2023) |
GnomAD
Source:
| 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:
- 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