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Intellectual disability

Gene: HIST1H4C

Green List (high evidence)

HIST1H4C (histone cluster 1 H4 family member c)
EnsemblGeneIds (GRCh38): ENSG00000197061
EnsemblGeneIds (GRCh37): ENSG00000197061
OMIM: 602827, Gene2Phenotype
HIST1H4C is in 4 panels

5 reviews

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Histone H4 is a core component of the nucleosome, the basic repeating unit of eukaryotic chromatin. Each nucleosome consists of ~150 bp of DNA wrapped around a histone octamer. Each histone octamer is composed of 2 copies of each of the histones H2A, H2B, H3, H4. This organization is important for DNA replication, transcription and repair.

There are 14 canonical histone H4 genes in the human genome, which despite being different at the nucleotide level encode an identical protein. These cluster in 3 genomic loci. Their transcription is independently regulated with differing expression during brain development and in human tissues.

Histone H4 forms a dimer with H3 (which however has variant isoforms linked to specific cellular processes).

Pathogenic variants in genes encoding H4 have been reported in several individuals. Irrrespective of the gene for H4 involved, all patients presented with highly overlapping features, DD and ID being universal. Available reports to date concern :
- H4C3/HIST1H4C (9 subjects - PMID: 28920961, 35202563),
- H4C11/HIST1H4J (1 subject - PMID: 31804630, 35202563),
- H4C4/HIST1H4D (1 subject - PMID:35202563),
- H4C5/HIST1H4E (17 subjects - PMID: 35202563),
- H4C6/HIST1H4F (1 subject - PMID: 35202563),
- H4C9/HIST1H4I (3 subjects - PMID: 35202563).

Variants in all cases were missense SNVs, occurring (in almost all cases) as dn variants and affecting the same residue in the same and/or different H4 genes (details for clusters below). Eg. Arg45Cys was a recurrent variant for H4C5 (>=7 subjects), while variants affecting Arg40 have been reported in H4C4, H4C5, H4C9, H4C11 (7 subjects overall).

Zebrafish studies for all genes reported have included most - if not all - patient variants and recapitulate features observed in affected individuals (head size/structure and growth).

Additional studies specificaly for H4C3/HIST1H4C have been performed in patient fibroblasts (demonstrating among others transcriptional dysregulation) and zebrafish (accumulation of DSBs, increased apoptosis in head/tail, abn. cell cycle progression).

Note that the nomenclature for variants - at the protein level - used in literature commonly takes into consideration cleavage of Met1, thus the numbering may not correspond to the HGVS one.

Relevant entries exist in OMIM, G2P and SysID only for H4C3/HIST1H4C (Tessadori-van Haaften neurodevelopmental syndrome 1, #619758) and H4C11/HIST1H4J (?Tessadori-van Haaften neurodevelopmental syndrome 2, #619759) but not for other genes.

Rating in PanelApp Australia - ID Panel : HIST1H4C Green, H4J Amber, H4D Amber, H4E Green, H4F Amber, H4I Green.

Please consider inclusion in other possibly relevant panels (microcephaly, short stature/FTT, etc).

Initial work from Tessadori et al (incl. DDD study, 2017 - PMID:28920961) identified monoallelic missense SNVs affecting the same residue of H4C3 (HIST1H4C), in 3 individuals from 2 families. [c.274A>C/ HGVS p.(Lys92Gln) dn in 1 subject and c.275A>C/ HGVS p.(Lys92Arg) inherited from unaffected mosaic parent].

Individuals from both families having relevant age had intellectual disability (2/2 - 2 families). Other features incl. growth delay (3/3) and microcephaly (3/3).

Expression of the variants in zebrafish severely affected structural development recapitulating the patient phenotypes (microcephaly and short stature).

RNA sequencing in fibroblasts from 2 unrelated patients and a control, revealed that expression of H4C3 variants was similar to wt. The authors estimated that ~8% of H4 cDNA molecules contained the variant. LC-MS/MS analysis suggested that the mutant protein was present in nucleosomes at a level of 1-2% while RNA-seq identified 115 differential expressed genes, with enrichment for relevant procedures (chr. organization, histone binding, DNA packaging, nucleosomal organization, cell cycle).

Post-translational modifications of Lys92 (H4K91) are highly conserved and have been previously associated with processes from chromatin assembly , DNA damage sensitivity, etc. Post-translational marks on Lys92 (K91) were absent in patient derived cells as a result of each variant.

Zebrafish models for both variants were suggestive for accumulation of double strand breaks (DSBs) more visible in heads and tails of larvae. Embryos expressing mutants displayed increased apoptosis in head and tail. Additional studies in larvae were suggestive of abnormal cell cycle progression (rel. increase in cellls in S/G2/M phase, increased occurrence of activated CHK2 with p53 stabilization) applying to both variants studied.

In a subsequent publication, Tessadori et al. (2020 - PMID: 31804630) described the phenotype of a 14 y.o. boy harboring a dn heterozygous missense H4C11 (HIST1H4J) variant following trio-ES [c.274A>G / HGVS p.(Lys92Glu)]. Features incl. profound ID, microcephaly, short stature with some dysmorphic features (uplsanting p-f, hypertelorism, etc). Previous work-up was normal/non-diagnostic and incl. FMR1, MECP2 and a CMA showing an inherited 207 kb CNV involving KCNV1. Upon mRNA microinjection in zebrafish embryos - either for wt or for Lys92Glu HIST1H4J - effect for wt was very mild. Lys92Glu expression led to defective development of head structures (brain, eyes), faulty body axis growth and dysmorphic tail reproducing the microcephaly and short stature phenotype. This was similar to previous zebrafish studies for HIS1H4C variants (above).

Tessadori et al. (2022 - PMID: 35202563) describe 29 *additional* individuals with de novo missense variants in genes encoding H4, namely:
- H4C3 (HIST1H4C/N=6 subjects),
- H4C11 (HIST1H4J/N=1),
- H4C4 (HIST1H4D/N=1),
- H4C5 (HIST1H4E/N=17),
- H4C6 (HIST1H4F/N=1),
- H4C9 (HIST1H4I/N=3).

All individuals, exhibited DD and ID (29/29). Other features incl. hypotonia (10/29), seizures (5/29), autism (5/29), ataxia (4/29). Abnormal growth incl. progressive microcephaly (2/19 prenatal, 20/29 postnatal onset), short stature/FTT (each 11/29). Few had skeletal features (craniosynostosis 2/29, abn. digits 4/29, vertebral 4/29). Some had visual (17/28) or hearing impairment (7/29). Facial features incl. hypertelorism (5/29), upslanting p-f (3/29), broad nasal tip (11/29), thin upper lip (4/29) and teeth anomalies (6/29 - notably gap between central incisors).

The authors state that the cohort was collected with trio WES but also after data sharing via Genematcher / DECIPHER.

Identified variants were in all cases missense and de novo, the latter either by trio WES or Sanger sequencing of parents.

Previous work-up or presence of additional variants are not discussed.

At the protein level 10 aa were affected, 6 of which recurrently within the same gene (Arg45, His75, Lys91, Tyr98) as well among several genes for H4 (Pro32, Arg40). Variants lied within two clusters, one corresponding to the α-helix of H4 (reported variants affected Lys31 - Arg45) important for DNA contacts, interactions with H3 and histone chaperones. The other within the core of nucleosome (reported patient variants : His75-Tyr98) with important strucural contact between H3-H4 dimer and histone chaperones.

There were no detectable genotype-phenotype patterns separating individual H4 genes or protein regions. Of note, variability was observed even among 7 individuals with the same dn H4C5 variant (Arg45Cys).

All variants were absent from control databases incl. gnomAD and affected residues conserved through to S. cerevisiae. Substitutions affecting Arg45 and Gly94 and His75 have been studied previously with effect in growth/fitness/chromatin remodeling/DNA damage repair depending on variant (5 studies cited).

Zebrafish embryos at the 1 cell stage were injected with mRNA encoding either wt or identified variants, the latter inducing significant developmental defects with the exception of Pro32Ala (H4C3) and Arg40Cys (H4C5, H4C11).

For Pro32Ala and Arg40Cys however, the strong recurrence in this cohort supports pathogenicity. A dosage dependent effect was observed for 2 variants.

H4 genes appear to be tolerant to both missense and loss-of-function variation (the latter even in homozygous form) suggesting a dominant effect of the variants.

[RefSeqs : H4C3/HIST1H4C - NM_0035242.4 | H4C4/HIST1H4D - NM_003539.4 | H4C5/HIST1H4E - NM_003545.3 | H4C6/HIST1H4F - NM_003540.4 | H4C9/HIST1H4I - NM_003495.2 | H4C11/HIST1H4J - NM_021968.4 // Variants at the protein level above are according to the HGVS nomenclature. However as the N-terminal methionine is cleaved, numbering relative to the mature peptide has also been used in publications eg. p.Pro33Ala HGVS corresponding to Pro32Ala]
Created: 18 Mar 2022, 3:50 p.m. | Last Modified: 18 Mar 2022, 3:50 p.m.
Panel Version: 3.1520

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Tessadori-van Haaften neurodevelopmental syndrome 1, #619758


Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

Sarah Leigh (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 14 Mar 2022, 2:22 p.m. | Last Modified: 14 Mar 2022, 2:22 p.m.
Panel Version: 3.1519

Ivone Leong (Genomics England Curator)

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 ( 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

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Only two families to date, considered appropriate for amber and watchlist.
Created: 5 Mar 2018, 12:38 p.m.

Louise Daugherty (Genomics England Curator)

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.


Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
  • Expert Review Green
  • Victorian Clinical Genetics Services
  • Gene2Phenotype
  • Tessadori-van Haaften neurodevelopmental syndrome 1, OMIM:619758
Clinvar variants
Variants in HIST1H4C
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Panels with this gene

History Filter Activity

10 May 2022, Gel status: 3

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: HIST1H4C were set to 28920961

10 May 2022, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: HIST1H4C were changed from Growth delay, microcephaly and intellectual disability to Tessadori-van Haaften neurodevelopmental syndrome 1, OMIM:619758

10 May 2022, Gel status: 3

Set mode of pathogenicity

Arina Puzriakova (Genomics England Curator)

Mode of pathogenicity for gene: HIST1H4C was changed from None to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

10 May 2022, Gel status: 3

Set mode of inheritance

Arina Puzriakova (Genomics England Curator)

Mode of inheritance for gene: HIST1H4C was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

14 Mar 2022, Gel status: 3

Removed Tag

Ivone Leong (Genomics England Curator)

Tag Q3_21_rating was removed from gene: HIST1H4C.

14 Mar 2022, Gel status: 3

Added New Source, Status Update

Ivone Leong (Genomics England Curator)

Source Expert Review Green was added to HIST1H4C. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

20 Sep 2021, Gel status: 2

Removed Tag, Added Tag

Ivone Leong (Genomics England Curator)

Tag watchlist was removed from gene: HIST1H4C. Tag Q3_21_rating tag was added to gene: HIST1H4C.

6 Sep 2019, Gel status: 2

Added Tag

Louise Daugherty (Genomics England Curator)

Tag new-gene-name tag was added to gene: HIST1H4C.

28 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to HIST1H4C.

12 Mar 2018, Gel status: 2

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

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.

12 Mar 2018, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

HIST1H4C was added to Intellectual disability panel. Sources: Expert Review Amber,Gene2Phenotype

12 Mar 2018, Gel status: 2


Ellen McDonagh (Genomics England Curator)

HIST1H4C was created by Ellen McDonagh