NM_018082.6(POLR3B):c.1568T>A (p.Val523Glu) AND Hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism
- Germline classification:
- Pathogenic (13 submissions)
- Last evaluated:
- Mar 1, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000032280.32
Allele description [Variation Report for NM_018082.6(POLR3B):c.1568T>A (p.Val523Glu)]
NM_018082.6(POLR3B):c.1568T>A (p.Val523Glu)
- Gene:
- POLR3B:RNA polymerase III subunit B [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 12q23.3
- Genomic location:
- Preferred name:
- NM_018082.6(POLR3B):c.1568T>A (p.Val523Glu)
- Other names:
- rs138249161; NM_018082.5(POLR3B):c.1568T>A; p.V523E
- HGVS:
- NC_000012.12:g.106432421T>A
- NG_031837.1:g.79764T>A
- NM_001160708.2:c.1394T>A
- NM_018082.6:c.1568T>AMANE SELECT
- NP_001154180.1:p.Val465Glu
- NP_001154180.1:p.Val465Glu
- NP_060552.4:p.Val523Glu
- NC_000012.11:g.106826199T>A
- NM_001160708.1:c.1394T>A
- NM_018082.5:c.1568T>A
- Q9NW08:p.Val523Glu
This HGVS expression did not pass validation- Protein change:
- V465E; VAL523GLU
- Links:
- UniProtKB: Q9NW08#VAR_067006; OMIM: 614366.0005; dbSNP: rs138249161
- NCBI 1000 Genomes Browser:
- rs138249161
- Molecular consequence:
- NM_001160708.2:c.1394T>A - missense variant - [Sequence Ontology: SO:0001583]
- NM_018082.6:c.1568T>A - missense variant - [Sequence Ontology: SO:0001583]
- Functional consequence:
- probably has functional consequence
- Observations:
- 2
Condition(s)
- Name:
- Hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism
- Synonyms:
- Hypomyelinating leukodystrophy 8, with or without oligodontia and/or hypogonadotropic hypogonadism; LEUKODYSTROPHY, HYPOMYELINATING, 8, WITH HYPODONTIA AND HYPOGONADOTROPIC HYPOGONADISM; Cerebellar hypoplasia with endosteal sclerosis; See all synonyms [MedGen]
- Identifiers:
- MONDO: MONDO:0013722; MedGen: C3280644; Orphanet: 85186; Orphanet: 88637; OMIM: 614381
-
Homo sapiens mRNA for polo-like kinase variant protein
Homo sapiens mRNA for polo-like kinase variant proteingi|62087937|dbj|AB209179.1|Nucleotide
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See more...Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000045453 | OMIM | no assertion criteria provided | Pathogenic (Nov 11, 2011) | germline | literature only | |
SCV000055916 | GeneReviews | no classification provided | not provided | germline | literature only | |
SCV000564291 | Biochimie-Hormonologie, Robert Debre Hospital | no assertion criteria provided | Pathogenic (Dec 21, 2016) | germline | clinical testing | |
SCV000744101 | Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus | criteria provided, single submitter (ACGS Guidelines, 2013) | Pathogenic (Jul 28, 2017) | germline | clinical testing | |
SCV000746009 | Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus | no assertion criteria provided (ACGS Guidelines, 2013) | Pathogenic (Jan 30, 2015) | germline | clinical testing | |
SCV001440438 | Institute of Human Genetics, University of Leipzig Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 1, 2019) | unknown | clinical testing | |
SCV001520343 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 21, 2022) | unknown | clinical testing | |
SCV001760291 | Genomics England Pilot Project, Genomics England | no assertion criteria provided (ACGS Guidelines, 2016) | Pathogenic | germline | clinical testing | |
SCV002761513 | Genetics and Molecular Pathology, SA Pathology
| criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 8, 2022) | germline | clinical testing | |
SCV003761423 | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Feb 24, 2022) | germline | curation | |
SCV003915645 | Undiagnosed Diseases Network, NIH | no assertion criteria provided | Pathogenic (Apr 1, 2022) | maternal | clinical testing | |
SCV004099015 | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Aug 2, 2023) | germline | clinical testing | |
SCV004814190 | Institute of Human Genetics, Heidelberg University | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 1, 2024) | maternal | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | literature only, curation |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | maternal | yes | 1 | not provided | not provided | not provided | not provided | clinical testing |
Causasians | germline | yes | 1 | not provided | not provided | not provided | not provided | clinical testing |
Citations
PubMed
Cerebellar hypoplasia with endosteal sclerosis is a POLR3-related disorder.
Ghoumid J, Petit F, Boute-Benejean O, Frenois F, Cartigny M, Vanlerberghe C, Smol T, Caumes R, de Roux N, Manouvrier-Hanu S.
Eur J Hum Genet. 2017 Aug;25(8):1011-1014. doi: 10.1038/ejhg.2017.73. Epub 2017 Jun 7.
- PMID:
- 28589944
- PMCID:
- PMC5567146
4H leukodystrophy caused by a homozygous POLR3B mutation: Further delineation of the phenotype.
Verberne EA, Dalen Meurs L, Wolf NI, van Haelst MM.
Am J Med Genet A. 2020 Jul;182(7):1776-1779. doi: 10.1002/ajmg.a.61600. Epub 2020 Apr 22.
- PMID:
- 32319736
- PMCID:
- PMC7318643
Details of each submission
From OMIM, SCV000045453.4
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (5) |
Description
In 3 unrelated patients of European descent with hypomyelinating leukodystrophy-8 with hypodontia and hypogonadotropic hypogonadism (HLD8; 614381), Tetreault et al. (2011) identified compound heterozygous mutations in the POLR3B gene. All had a heterozygous 1568T-A transversion in exon 15, resulting in a val523-to-glu (V523E) substitution. The other POLR3B mutations found in compound heterozygosity with V523E were a 1508C-A transversion in exon 15, resulting in a thr503-to-lys (T503K; 614366.0006) substitution; a 1-bp deletion (1533delT; 614366.0007) predicted to result in a frameshift and premature stop codon; and a 2686A-T transversion in exon 23, resulting in a lys896-to-ter (K896X; 614366.0008) substitution. Based on electron microscopy structure, the V523E and T503K substitutions were predicted be located near the 'jaw' of pol III, where other subunits are localized. Thus these mutations would affect local structure and impair proper function of pol III. None of the mutations were found in 340 control chromosomes, except for V523E, which was found in 2 (0.5%) of 374 control chromosomes. All patients presented in early childhood with mild developmental delays and developed dysarthria as well as progressive motor difficulties, including cerebellar ataxia. Two showed progressive spasticity. Two individuals developed hypogonadotropic hypogonadism, whereas the third was too young to evaluate for endocrine dysfunction. All 3 individuals had teeth abnormalities, such as neonatal upper incisors, delayed eruption of deciduous teeth and permanent teeth, abnormal sequence of eruption, and malposition. Brain MRI showed thin corpus callosum, cerebellar atrophy, and hypomyelination.
Wolf et al. (2014) reported that 51 of 62 patients with HLD8 were compound heterozygous for the V523E variant and another mutation in the POLR3B gene. Only 1 sib pair was homozygous for V523E, and the sibs had an exceptionally mild clinical course, with the older sib having no neurologic signs at age 21 years. Brain MRI in the sibs showed much better myelination in the 2 homozygous sibs than in the other patients.
In 2 unrelated patients (patients 8 and 9) with HLD8, Daoud et al. (2013) identified compound heterozygous mutations in the POLR3B gene: V523E and a c.2084-6A-G transition (IVS19-6A-G; 614366.0016) in intron 19, resulting in creation of a cryptic splice site and leading to a frameshift and premature termination (Gly695ValfsTer5). The mutations were identified by sequencing of the POLR3B gene. The V523E variant had an allele frequency of 0.5% in the dbSNP database.
In a 15-year-old boy with HLD8, Ghoumid et al. (2017) identified compound heterozygous mutations in the POLR3B gene: V523E and a c.2274T-C transition resulting in a pro925-to-gln (P925Q; 614366.0015) substitution at a conserved site. The mutations were identified by Sanger sequencing of the POLR3B gene. The P925Q mutation was predicted to modify protein conformation. It was not present in the ExAC database.
In a 21-year-old Dutch Caribbean woman with HLD8, Verberne et al. (2020) identified homozygosity for the V523E mutation. The mutation was found by sequencing of a gene panel of 761 genes associated with intellectual disability. Both parents were heterozygous for the mutation. The mutation was present in the gnomAD database at an allele frequency of 0.0003%. The patient had ataxia, developmental delay, and impaired intellectual development.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From GeneReviews, SCV000055916.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (5) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Biochimie-Hormonologie, Robert Debre Hospital, SCV000564291.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | Causasians | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000744101.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV000746009.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440438.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was identified as compound heterozygous.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Baylor Genetics, SCV001520343.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genomics England Pilot Project, Genomics England, SCV001760291.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genetics and Molecular Pathology, SA Pathology, SCV002761513.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (4) |
Description
The POLR3B c.1568T>A variant is classified as Pathogenic (PS4, PM2, PM3_Strong, PP3) The POLR3B c.1568T>A variant is a single nucleotide change in exon 15/28 of the POLR3B gene, which is predicted to change the amino acid valine at position 523 in the protein to glutamic acid. The variant has been reported in probands with a clinical presentation of Leukodystrophy. POLR3B:c.1568T>A has been described in the scientific literature in multiple patients with diffuse gastric cancer (Tétreault, et al, 2011, PMID: 22036172; Daoud et al., 2013 PMID: 23355746) (PS4). The variant is rare in population databases (PM2).This variant has been reported as compound heterozygous with another pathogenic variant, (POLR3B:c.2084-6A>G: clinvar ID 419962, POLR3B):c.2570+1G>A: clinvar ID 620581) in multiple unrelated individuals with POLR3B related leukodystrophy (Wolf et al., 2014, PMID:25339210) (PM3_Strong)
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761423.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | curation | PubMed (1) |
Description
The p.Val523Glu variant in POLR3B has been reported in >10 individuals with 4H leukodystrophy (PMID: 22036172, 25339210, 23355746), segregated with disease in 4 affected relatives from 4 families (PMID: 25339210), and has been identified in 0.06% (78/128850) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs138249161). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID#: 31166) and has been interpreted as pathogenic by multiple submitters. Of the many affected individuals, 1 of those were homozygote and 3 were compound heterozygotes that carried reported likely pathogenic variants in trans and with unknown phase, which increases the likelihood that the p.Val523Glu variant is pathogenic (VariationID: 1184082, 1184071, 31167; PMID: 22036172, 25339210, 23355746). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The number of missense variants reported in POLR3B in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive 4H leukodystrophy. ACMG/AMP Criteria applied: PP3, PP1_strong, PM3_strong, PP2 (Richards 2015).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Undiagnosed Diseases Network, NIH, SCV003915645.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | maternal | yes | not provided | Blood | not provided | 1 | not provided | not provided | not provided |
From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV004099015.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
PM2, PM3_Very Strong, PP2, PP3
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, Heidelberg University, SCV004814190.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | maternal | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Nov 10, 2024