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Intellectual disability

Gene: H3F3A

Amber List (moderate evidence)

H3F3A (H3 histone family member 3A)
EnsemblGeneIds (GRCh38): ENSG00000163041
EnsemblGeneIds (GRCh37): ENSG00000163041
OMIM: 601128, Gene2Phenotype
H3F3A is in 5 panels

3 reviews

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Upgraded from Red to Amber, but there is sufficient evidence to promoted to Green at the next GMS panel update (added 'for-review' tag).

Multiple unrelated cases (>30) with GDD/ID associated with de novo variants in this gene.
Created: 22 Dec 2020, 4:26 p.m. | Last Modified: 22 Dec 2020, 4:26 p.m.
Panel Version: 3.670
Currently not associated with any phenotype in OMIM, but is listed in Gene2Phenotype with a 'confirmed' disease confidence rating for 'Craniofacial with neurodevelopment disorders'.

- PMID: 31942419 (2019) - De novo missense variant identified by trio exome sequencing in a girl with secondary microcephaly, severe DD and ID, growth retardation and dysmorphic features. Brain MRI demonstrated hypoplasia of corpus callosum and cerebellum as well as thin layer of frontal and parietal periventricular gliosis. No functional analyses of the variant or patient cells were performed.

- PMID: 33268356 (2020) - De novo missense variants identified in 33 unrelated individuals with a shared phenotype of GDD/ID, usually severe and often progressive, with mostly minor congenital anomalies. 23/28 patients showed abnormalities on brain MRI including hypoplasia/agenesis of the corpus collosum (9), cortical atrophy (6) and impaired myelination (5). Variable seizure phenotypes were reported in 17/33 cases, all early-onset where specified, mostly during infancy (latest onset at 14 years of age).
Created: 22 Dec 2020, 4:20 p.m. | Last Modified: 22 Dec 2020, 4:20 p.m.
Panel Version: 3.669

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Developmental delay; Neurodegeneration; Epilepsy; Facial dysmorphism; Congenital anomalies

Publications

Zornitza Stark (Australian Genomics)

Green List (high evidence)

33 unrelated individuals reported with missense variants in H3F3A. Phenotype primarily comprised intellectual disability and minor congenital anomalies, regression in significant proportion. Seizures in 50%.
Created: 9 Dec 2020, 7:31 a.m. | Last Modified: 9 Dec 2020, 7:31 a.m.
Panel Version: 3.644

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Intellectual disability; regression; seizures

Publications

Louise Daugherty (Genomics England Curator)

Added new-gene-name tag, new approved HGNC gene symbol for H3F3A is H3-3A
Created: 6 Sep 2019, 3:43 p.m. | Last Modified: 6 Sep 2019, 3:43 p.m.
Panel Version: 2.1022

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Victorian Clinical Genetics Services
Phenotypes
  • Developmental delay
  • Intellectual disability
  • Neurodegeneration
  • Epilepsy
  • Facial dysmorphism
  • Congenital anomalies
Tags
new-gene-name for-review
OMIM
601128
Clinvar variants
Variants in H3F3A
Penetrance
None
Publications
Panels with this gene

History Filter Activity

22 Dec 2020, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: H3F3A were changed from to Developmental delay; Intellectual disability; Neurodegeneration; Epilepsy; Facial dysmorphism; Congenital anomalies

22 Dec 2020, Gel status: 2

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: H3F3A were set to

22 Dec 2020, Gel status: 2

Set mode of inheritance

Arina Puzriakova (Genomics England Curator)

Mode of inheritance for gene: H3F3A was changed from to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

22 Dec 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: h3f3a has been classified as Amber List (Moderate Evidence).

22 Dec 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: h3f3a has been classified as Amber List (Moderate Evidence).

22 Dec 2020, Gel status: 1

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review tag was added to gene: H3F3A.

6 Sep 2019, Gel status: 1

Added Tag

Louise Daugherty (Genomics England Curator)

Tag new-gene-name tag was added to gene: H3F3A.

28 Sep 2018, Gel status: 1

Created, Added New Source, Set mode of inheritance

Louise Daugherty (Genomics England Curator)

gene: H3F3A was added gene: H3F3A was added to Intellectual disability. Sources: Victorian Clinical Genetics Services Mode of inheritance for gene: H3F3A was set to