ASH1L
protein-codingASH1 like histone lysine methyltransferase, the group of Bromodomain containing|Lysine methyltransferases|PHD finger proteins|SET domain containing|MicroRNA protein coding host genes
Gene summary
This gene encodes a member of the trithorax group of transcriptional activators. The protein contains four AT hooks, a SET domain, a PHD-finger motif, and a bromodomain. It is localized to many small speckles in the nucleus, and also to cell-cell tight junctions. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~227.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0015802
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0030918
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0030918
Submitter: Illumina
The ASH1L gene is located on chromosome 1 at 1q22 and encodes the ASH1 like histone lysine methyltransferase protein, which is responsible for methylating Lys-36 of histone H3. ASH1L was first reported in relation to autosomal dominant ASH1L-related intellectual disability in 2012 (23033978: de Ligt et al. 2012). At least six unique de novo variants have been reported, including missense, frameshift, stop-gained variants. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Variants in this gene have been reported in at least six probands in three publications (23033978: de Ligt et al. 2012; 28191889: Stessman et al. 2017; 29276005: Faundes et al. 2018). More evidence is available in the literature, but the maximum score for genetic evidence has been reached. This gene-disease association is supported by somewhat limited experimental evidence, including expression of ASH1a in the zebrafish brain and during early epiphysial neurogenesis and a null zebrafish model that demonstrates importance of ASH1a in neurogenesis in zebrafish (12702659: Cau and Wilson 2003). In summary, there is strong evidence to support the relationship between ASH1L and autosomal dominant ASH1L-related intellectual disability.
Inheritance Pattern: AD
Disease ID:MONDO:0030918
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0030918
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0800439
Submitter: ClinGen
*ASH1L* was first reported in relation to an autosomal dominant intellectual disability disorder in 2012 (de Ligt et al., PMID: 23033978). Phenotypes are variable with most probands having intellectual disability or developmental delay, autism spectrum disorder, variable dysmorphic features, and behavioral problems including attention deficit hyperactivity disorder and self-injurious behavior. Less prevalent features include cryptorchidism, penile torsion, abnormal brain MRI, hypotonia, seizures, pectus, scoliosis, cervical spine fusion, hyperopia, strabismus, nystagmus, and ptosis (PMIDs: 29753921, 28394464, 34373061, 23033978, 29276005, 28191889). This gene has been curated under the disease entity syndromic complex neurodevelopmental disorder. There are nine *de novo* heterozygous variants found in nine probands reported in six publications (PMIDs: 29753921, 28394464, 34373061, 23033978, 29276005, 28191889) included in this curation. Of these, seven variants are nonsense or frameshift, supporting a hypothesized disease mechanism of haploinsufficiency; two additional variants included here are missense, but no functional studies were performed. Of note, two additional probands are available from the Brain Gene Registry (braingeneregistry.wustl.edu); the variants identified in these individuals are not formally documented in this curation due to technical limitations, but they are available in ClinVar (ClinVar IDs: SCV003927994.1 and SCV003927995.1). These individuals, one presenting with a *de novo* frameshift variant and one with a *de novo* nonsense variant, added the phenotypes of ataxic gait, mixed-receptive language disorder, anxiety, and depression to the phenotypic spectrum. At present, there is no experimental evidence to support the gene-disease relationship. Two mouse models have been reported in the literature but have not been scored as they did not sufficiently recapitulate the human disease phenotype. In summary, there is definitive evidence to support the relationship between *ASH1L* and syndromic complex neurodevelopmental disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the Intellectual Disability and Autism Gene Curation Expert Panel on February 23, 2023 (SOP 9).
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ASH1L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018489.3. 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 | 15 | 84 | 12 | 111 | ||
| missense | 2 | 4 | 730 | 107 | 7 | 850 |
| nonsense | 26 | 19 | 7 | 2 | 54 | |
| start loss | 0 | |||||
| frameshift | 33 | 29 | 4 | 66 | ||
| splice donor/acceptor (+/-2bp) | 3 | 9 | 12 | |||
| Total | 64 | 52 | 765 | 193 | 19 | 1093 |
Highest pathogenic variant AF is 0.000019826444
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060959.2 | 27 | MANE Select | |
| Ensembl | ENSP00000376204.3 | 27 | MANE Select | |
| RefSeq | NP_001353106.1 | 27 | Standard | |
| Ensembl | ENSP00000357330.3 | 27 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Lysine degradation - Homo sapiens (human)
- Histone Modifications
- PKMTs methylate histone lysines
- Chromatin modifying enzymes
- Lysine metabolism
Biological Process
- skeletal system development
- negative regulation of acute inflammatory response
- DNA packaging
- transcription by RNA polymerase II
- cell-cell signaling
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA binding
- chromatin binding
- histone-lysine N-methyltransferase activity
- histone methyltransferase activity (H3-K4 specific)
Cellular Component
- nucleus
- nucleoplasm
- chromosome
- Golgi apparatus
- bicellular tight junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000392403
- Coding exons
- 27
- Length
- 227540
- Individuals with no LoFs
- 125739
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125746
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.47 | 1179 | 1.57e+3 | 0.753 | 0.0000862 | 19455 |
| Missense (PolyPhen) | 514 | 817.3 | 0.6289 | 10032 | ||
| Synonymous | 1.24 | 518 | 555 | 0.933 | 0.0000278 | 5759 |
| Loss of Function | 10.1 | 3 | 125 | 0.0239 | 0.00000829 | 1557 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Histone methyltransferase specifically methylating 'Lys- 36' of histone H3 (H3K36me). {ECO:0000269|PubMed:21239497}.;
- Disease
- DISEASE: Mental retardation, autosomal dominant 52 (MRD52) [MIM:617796]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:27824329, ECO:0000269|PubMed:28191889, ECO:0000269|PubMed:28394464}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- LoFtool
- 0.00737
- RVIS EVS
- -1.8
- RVIS percentile EVS
- 2.22
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.790
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |