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Intellectual disability

Gene: HEATR3

Amber List (moderate evidence)
HEATR3 (HEAT repeat containing 3)
EnsemblGeneIds (GRCh38): ENSG00000155393
EnsemblGeneIds (GRCh37): ENSG00000155393
OMIM: 614951, Gene2Phenotype
HEATR3 is in 5 panels

2 reviews

Sarah Leigh (Genomics England Curator)

I don't know

Comment on list classification: The amber rating reflects that mild ID has been associated with HEATR3 variants.
Created: 8 Sep 2022, 9:02 a.m. | Last Modified: 8 Sep 2022, 9:02 a.m.
Panel Version: 3.1702
Not associated with a phenotype in OMIM, Gen2Phen or MONDO. PMID: 35213692 reports five HEATR3 variants in four unrelated cases.
Created: 25 Aug 2022, 9:50 a.m. | Last Modified: 25 Aug 2022, 9:50 a.m.
Panel Version: 3.1685
Created: 25 Aug 2022, 9:50 a.m.
Last Modified: 25 Aug 2022, 9:50 a.m.
Panel version: 3.1685

Konstantinos Varvagiannis (Other)

I don't know

O'Donohue et al (2022 - PMID: 35213692) describe the clinical features of 6 individuals (from 4 unrelated families) with biallelic pathogenic HEATR3 variants.

These included bone marrow failure (anemia/anemia and thrombocytopenia at presentation), short stature/growth retardation (4/6), facial features (5/6 - in some: straight eyebrows, d-s palpebral fissures, synophrys) and skeletal findings incl. disproportionately short fingers/thumb anomaly. ID was reported in 4/6 individuals from 3 families (all: mild ID | 2/6 without ID). The phenotype corresponded overall to a variant form Diamond-Blackfan anemia (DBA, disorder caused by variants in genes encoding for ribosomal proteins) with additional features.

The 1st family (2 affected sibs and parents) underwent WES, not diagnostic for DBA. Analysis suggested variants in HEATR3 (prioritized due to its potential role in ribosome biogenesis) and 4 additional genes as candidates. Collaboration in the European DBA consortium and national DBA consortia led to identification of additional families.

HEATR3 encodes Heat-repeat-containing protein 3 or symportin, a protein that co-imports uL5 (encoded by RPL11) and uL18 (RPL5) in the nucleus where they assemble with 5S rRNA to form 5S RNP. The 5S RNP complex incorporates with maturing large ribosomal subunits to form the central protuberance. When 5S RNP is not incorporated, it accumulates and associates with Hdm2 ubiquitin ligase, the later normally targeting p53 proteasomal degradation.

The following missense and splice variants were identified (NM_182922):
- c.1751G>Α/p.(Gly584Glu) hmz
- c.1337G>A/p.(Cys446Tyr) hmz
- c.399+1G>T in trans with c.719C>T/p.(Pro240Leu)
- c.400T>C/p.(Cys134Arg) hmz

Variants were confirmed with Sanger sequencing. They were dispersed across HEATR3 without clustering although they affect residues either in the ARM (38-320) or HEAT (415-675) repeat domains, at positions evolutionary conserved, with in silico predictions in favor of a deleterious effect. With the exception of Cys134Arg (AF:4.11x10-6/no hmz), all were absent from gnomAD.

Studies in yeast suggested that deletions in symportin gene (syo1) lead to a mild growth defect and accumulation of 40S subunits. Similarly, two yeast strains engineered to test for the effect of the p.Gly584Glu (yeast p.Gly522Glu/Ala) exhibited growth defect and ribosomal subunit imbalance, both restored by wt Syo1.

HA-tagged HEATR3 in HeLa cells suggested that the co-translational capture mechanism to chaperone uL18 (RPL5) is conserved in human cells but was not observed upon expression of the p.Cys446Tyr variant.

While HEATR3 transcription was not affected in LCLs from individuals hmz for Gly584Glu or Cys446Tyr, protein levels were barely detectable, suggesting destabilization of the protein.

While uL18 accumulates in cytoplasm and nucleus with expected enrichment in nucleolus, upon siRNA knockdown of HEATR3 in HeLa cells this enrichment was lost. Studies in fibroblasts (Gly584Glu) demonstrated reduced uL18 nuclear staining. Overall, HEATR3 was suggested to be important for nuclear import of uL18 (though not for uL5).

LCL studies demonstrated pre-rRNA processing defects in patient cells with accumulation of 32S and 12S pre-rRNAs, the former being reminiscent of accumulations observed in individuals with RPL5- and RPL11-related DBA. Expression of wt HEATR3 restored processing defects.

LCLs from affected individuals revealed loss of free 60S subunits (as in yeast) with expression of wt cDNA restoring Nl levels.

Western blots of LCLs demonstrated that the levels of uL5, uL18 and p53 were not affected (the latter also observed in RPL5-related DBA)

Studies of bone marrow smears from 2 affected individuals allowed to conclude in a strong defect in erythroid cell proliferation.

Currently, there is no HEATR3-associated phenotype in OMIM, PanelApp Australia, G2P or the SysID database.

Consider inclusion in the ID panel with amber (mild ID in >3 individuals/families/variants although not universal feature) or green rating. Also consider inclusion in other possibly relevant panels eg. for cytopenias/congenital anemias, short stature, etc.
Sources: Literature
Created: 11 Mar 2022, 9:50 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Anemia; Thrombocytopenia; Growth delay; Short stature; Abnormality of the skeletal system; Abnormality of finger; Abnormality of the thumb; Intellectual disability; Obesity; Abnormality of the face

Publications

Created: 11 Mar 2022, 9:50 a.m.

Panel version: 3.1518

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • Anemia
  • Thrombocytopenia
  • Growth delay
  • Short stature
  • Abnormality of the skeletal system
  • Abnormality of finger
  • Abnormality of the thumb
  • Intellectual disability
  • Obesity
  • Abnormality of the face
OMIM
614951
Clinvar variants
Variants in HEATR3
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

8 Sep 2022, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: heatr3 has been classified as Amber List (Moderate Evidence).

25 Aug 2022, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: heatr3 has been classified as Amber List (Moderate Evidence).

11 Mar 2022, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: HEATR3 was added gene: HEATR3 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: HEATR3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: HEATR3 were set to 35213692 Phenotypes for gene: HEATR3 were set to Anemia; Thrombocytopenia; Growth delay; Short stature; Abnormality of the skeletal system; Abnormality of finger; Abnormality of the thumb; Intellectual disability; Obesity; Abnormality of the face Penetrance for gene: HEATR3 were set to Complete Review for gene: HEATR3 was set to AMBER