Intellectual disabilityGene: HIST1H4C Amber List (moderate evidence)
Green List (high evidence)
This gene is associated with a phenotype in Gene2Phenotype (possible) but not OMIM. There is a third case identified internally at Victorian Clinical Genetics Services (https://panelapp.agha.umccr.org/panels/250/gene/HIST1H4C/). Therefore, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Created: 20 Sep 2021, 2:02 p.m. | Last Modified: 20 Sep 2021, 2:02 p.m.
Panel Version: 3.1283
Comment when marking as ready: Only two families to date, considered appropriate for amber and watchlist.
Created: 5 Mar 2018, 12:38 p.m.
Added new-gene-name tag, new approved HGNC gene symbol for HIST1H4C is H4C3
Created: 6 Sep 2019, 3:29 p.m. | Last Modified: 6 Sep 2019, 3:29 p.m.
Panel Version: 2.1022
This is a probable DD gene in Gene2Phenotype for a HIST1H4C Disease, all missense/in frame variants.
Created: 20 Feb 2018, 3:36 p.m.
Comment on list classification: Currently only two unrelated cases to support HIST1H4C variants causing an observed ID phenotype. There is also animal model in zebrafish that supports the observed phenotype in the patients.
Created: 20 Feb 2018, 3:23 p.m.
added watchlist tag
Created: 20 Feb 2018, 3:12 p.m.
Comment on phenotypes: added phenotypes as listed in PMID:28920961
Created: 20 Feb 2018, 3:12 p.m.
Comment on publications: added publication to support possible association to ID. Tessadori F, et al., 2017 (PMID: 28920961) reported monoallelic missense mutations affecting lysine 91 in the histone H4 core (H4K91) in 2 individuals (3 affecteds) with a syndrome of growth delay, microcephaly and intellectual disability.
The results highlight the alteration of K91 on histone H4 acts in a genetically dominant manner the results suggest a mechanism involving inherent DNA damage accumulation and early perturbation of the cell cycle, through which missense mutations in HIST1H4C affecting K91 of histone H4 are causative for an identifiable syndrome consisting of dysmorphic features and intellectual disability.
They concluded that the presence of two siblings (patients 2 and 3) from unrelated Dutch parents and another independent patient (patient 1) displaying similar clinical phenotypes, in combination with in vivo modeling evidence in zebrafish embryos, indicates that the substitutions affecting the gene HIST1H4C cause the abnormal phenotypes in patients.
Created: 20 Feb 2018, 2:52 p.m.
Tag watchlist was removed from gene: HIST1H4C. Tag Q3_21_rating tag was added to gene: HIST1H4C.
Tag new-gene-name tag was added to gene: HIST1H4C.
Source Victorian Clinical Genetics Services was added to HIST1H4C.
12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.
HIST1H4C was added to Intellectual disability panel. Sources: Expert Review Amber,Gene2Phenotype
HIST1H4C was created by Ellen McDonagh
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at [email protected]
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.