ASH1L

protein-coding

ASH1 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

NM_018489.3

Inheritance

AD

ClinVar variants

P:116U:765B:212

Top phenotype

Intellectual developmental disorder, autosomal dominant 52

gnomAD constraint

pLI —, LoF o/e 0.02

Max pathogenic AF

—

Genomic locus

chr1:155,335,268-155,563,162

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~227.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autosomal dominant non-syndromic intellectual disabilitySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015802

Submitter: Orphanet

intellectual developmental disorder, autosomal dominant 52STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030918

Submitter: G2P

intellectual developmental disorder, autosomal dominant 52STRONG

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.

intellectual developmental disorder, autosomal dominant 52STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030918

Submitter: Labcorp Genetics (formerly Invitae)

intellectual developmental disorder, autosomal dominant 52STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030918

Submitter: PanelApp Australia

syndromic complex neurodevelopmental disorderDEFINITIVE

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)

Intellectual developmental disorder, autosomal dominant 52AD

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

Refs: 23033978; 25961944; 27824329; 28191889; 28394464Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ASH1L variants in ClinVar

16 Conditions Cataloged
not providedTotal: 525
Inborn genetic diseasesTotal: 280
Intellectual disability, autosomal dominant 52Total: 243
ASH1L-related disorderTotal: 110
not specifiedTotal: 79
Intellectual disabilityTotal: 14
See casesTotal: 9
Syndromic complex neurodevelopmental disorderTotal: 5

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.

EffectPLPVUSLBBSum
synonymous
15
clinvar
84
clinvar
12
clinvar
111
missense
2
clinvar
4
clinvar
730
clinvar
107
clinvar
7
clinvar
850
nonsense
26
clinvar
19
clinvar
7
clinvar
2
clinvar
54
start loss
0
frameshift
33
clinvar
29
clinvar
4
clinvar
66
splice donor/acceptor (+/-2bp)
3
clinvar
9
clinvar
12
Total6452765193191093

Highest pathogenic variant AF is 0.000019826444

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_018489.3RefSeqNP_060959.227MANE Select
ENST00000392403.8EnsemblENSP00000376204.327MANE Select
NM_001366177.2RefSeqNP_001353106.127Standard
ENST00000368346.7EnsemblENSP00000357330.327Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.4711791.57e+30.7530.000086219455
Missense (PolyPhen)514817.30.628910032
Synonymous1.245185550.9330.00002785759
Loss of Function10.131250.02390.000008291557

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.0000990.000099rare
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000260.000026rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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