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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 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no 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
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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000045453OMIM
no assertion criteria provided
Pathogenic
(Nov 11, 2011)
germlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV000055916GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV000564291Biochimie-Hormonologie, Robert Debre Hospital
no assertion criteria provided
Pathogenic
(Dec 21, 2016)
germlineclinical testing

SCV000744101Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus
criteria provided, single submitter

(ACGS Guidelines, 2013)
Pathogenic
(Jul 28, 2017)
germlineclinical testing

Citation Link,

SCV000746009Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus
no assertion criteria provided

(ACGS Guidelines, 2013)
Pathogenic
(Jan 30, 2015)
germlineclinical testing

Citation Link,

SCV001440438Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 1, 2019)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001520343Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 21, 2022)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001760291Genomics England Pilot Project, Genomics England
no assertion criteria provided

(ACGS Guidelines, 2016)
Pathogenicgermlineclinical testing

Citation Link,

SCV002761513Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 8, 2022)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV003761423Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 24, 2022)
germlinecuration

PubMed (1)
[See all records that cite this PMID]

SCV003915645Undiagnosed Diseases Network, NIH
no assertion criteria provided
Pathogenic
(Apr 1, 2022)
maternalclinical testing

SCV004099015Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 2, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004814190Institute of Human Genetics, Heidelberg University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 1, 2024)
maternalclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedliterature only, curation
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedmaternalyes1not providednot providednot providednot providedclinical testing
Causasiansgermlineyes1not providednot providednot providednot providedclinical 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.

PubMed [citation]
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.

PubMed [citation]
PMID:
32319736
PMCID:
PMC7318643
See all PubMed Citations (9)

Details of each submission

From OMIM, SCV000045453.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000055916.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (5)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Biochimie-Hormonologie, Robert Debre Hospital, SCV000564291.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Causasians1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000744101.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV000746009.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440438.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was identified as compound heterozygous.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001520343.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Genomics England Pilot Project, Genomics England, SCV001760291.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genetics and Molecular Pathology, SA Pathology, SCV002761513.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761423.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration 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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Undiagnosed Diseases Network, NIH, SCV003915645.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providedBloodnot provided1not providednot providednot provided

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV004099015.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

PM2, PM3_Very Strong, PP2, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, Heidelberg University, SCV004814190.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024