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NM_000157.4(GBA1):c.1342G>C (p.Asp448His) AND Gaucher disease perinatal lethal

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Apr 1, 2020
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:
RCV000004526.21

Allele description [Variation Report for NM_000157.4(GBA1):c.1342G>C (p.Asp448His)]

NM_000157.4(GBA1):c.1342G>C (p.Asp448His)

Genes:
LOC106627981:GBA recombination region [Gene]
GBA1:glucosylceramidase beta 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q22
Genomic location:
Preferred name:
NM_000157.4(GBA1):c.1342G>C (p.Asp448His)
Other names:
D409H
HGVS:
  • NC_000001.11:g.155235727C>G
  • NG_009783.1:g.13971G>C
  • NG_042867.1:g.2189C>G
  • NM_000157.3(GBA):c.1342G>C
  • NM_000157.4:c.1342G>CMANE SELECT
  • NM_001005741.3:c.1342G>C
  • NM_001005742.3:c.1342G>C
  • NM_001171811.2:c.1081G>C
  • NM_001171812.2:c.1195G>C
  • NP_000148.2:p.Asp448His
  • NP_001005741.1:p.Asp448His
  • NP_001005742.1:p.Asp448His
  • NP_001165282.1:p.Asp361His
  • NP_001165283.1:p.Asp399His
  • NC_000001.10:g.155205518C>G
  • NM_000157.3(GBA):c.1342G>C
  • NM_000157.3:c.1342G>C
  • NM_000157.4:c.1342G>C
  • NM_001005741.2:c.1342G>C
  • NM_001005741.3:c.1342G>C
  • NM_001005742.2:c.1342G>C
  • NM_001005742.3:c.1342G>C
  • P04062:p.Asp448His
  • c.1342G>C (p.Asp448His)
Protein change:
D361H; ASP409HIS
Links:
UniProtKB: P04062#VAR_003313; OMIM: 606463.0006; OMIM: 606463.0047; dbSNP: rs1064651
NCBI 1000 Genomes Browser:
rs1064651
Molecular consequence:
  • NM_000157.4:c.1342G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005741.3:c.1342G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005742.3:c.1342G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171811.2:c.1081G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171812.2:c.1195G>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Gaucher disease perinatal lethal
Synonyms:
Gaucher disease collodion type; Gaucher disease, perinatal-lethal form
Identifiers:
MONDO: MONDO:0011945; MedGen: C1842704; OMIM: 608013

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000024700OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2008)
germlineliterature only

PubMed (13)
[See all records that cite these PMIDs]

SCV001366383Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 1, 2020)
unknownclinical testing

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

SCV003922073Lifecell International Pvt. Ltd
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
Asiangermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Glucocerebrosidase mutations in Gaucher disease.

Beutler E, Demina A, Gelbart T.

Mol Med. 1994 Nov;1(1):82-92.

PubMed [citation]
PMID:
8790604
PMCID:
PMC2229932

Gaucher disease: molecular heterogeneity and phenotype-genotype correlations.

Theophilus B, Latham T, Grabowski GA, Smith FI.

Am J Hum Genet. 1989 Aug;45(2):212-25.

PubMed [citation]
PMID:
2502917
PMCID:
PMC1683351
See all PubMed Citations (15)

Details of each submission

From OMIM, SCV000024700.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (13)

Description

Kurolap et al. (2019) noted that the ASP409HIS mutation is annotated as ASP448HIS (D448H), resulting from a c.1342G-C transversion (c.1342G-C, NM_000157.3) in the GBA gene. The sequence includes the 39-residue signal peptide.

The asp409-to-his (D409H) substitution in exon 9 of the GBA gene has also been reported as resulting from a c.957G-C transversion, based on a different reference sequence (Beutler, 1992).

Theophilus et al. (1989) identified a heterozygous D409H mutation in the GBA gene in 2 patients with type I Gaucher disease (230800) and 1 patient with type III (231000) Gaucher disease.

Cormand et al. (1995) identified heterozygosity for the D409H allele in Spanish patients with types I, II (230900), and III Gaucher disease. All patients had markedly different clinical phenotypes. Cormand et al. (1995) found that the D409H mutation accounted for 4 (5.7%) of 70 mutated alleles among 35 Spanish patients with Gaucher disease.

Chabas et al. (1995) described 3 Spanish sisters with an unusual form of Gaucher disease, later designated type IIIC (231005) (Bohlega et al., 2000), due to a homozygous D409H substitution in the GBA gene. Hepatosplenomegaly was present in all 3 sibs; characteristic Gaucher cells were found on bone marrow aspirate in 2 and in the splenectomy specimen in the third. The patients had cardiovascular abnormalities consisting of calcification of the ascending aorta and of the aortic and mitral valves. Neurologic findings included ophthalmoplegia and saccadic eye movements in 2 of the sisters, and tonic-clonic seizures in the third. The 3 sisters died at ages 16, 15, and 13, 2 of them having undergone aortic valve replacement.

Uyama et al. (1997) identified the homozygous D409H mutation in 3 Japanese adult sibs reported by Uyama et al. (1992) who had Gaucher disease associated with supranuclear ophthalmoplegia and cardiovascular calcifications.

Homozygosity for the D409H mutation has been reported in Arab (Abrahamov et al., 1995) and British/German (Beutler et al., 1995) patients with Gaucher disease and cardiovascular calcifications. These reports demonstrate a particularly tight pan-ethnic association between phenotype and genotype in this variant form of Gaucher syndrome.

Bohlega et al. (2000) described 4 Saudi Arabian sibs with the D409H mutation who had impaired horizontal saccades and aortic and mitral valve calcification without other systemic disease. Bohlega et al. (2000) suggested the designation 'Gaucher disease type IIIC.'

Inui et al. (2001) reported a patient who was compound heterozygous for the D409H allele and another unidentified mutation. He had hydrocephalus, corneal opacities, deformed toes, and cardiac features typical of patients who are homozygous for this allele. However, he also had fibrous thickening of the splenic and hepatic capsules and massive hepatosplenomegaly, features which differed from patients homozygous for the D409H allele. Enzyme replacement therapy was given for 4 years, resulting in an improvement of visceral and hematologic abnormalities but no neurologic improvement.

Mignot et al. (2003) identified the D409H mutation in compound heterozygosity with another mutation in a fetus with perinatal lethal Gaucher disease (608013).

Emre et al. (2008) identified homozygosity for the D409H mutation in 2 unrelated Turkish patients with Gaucher disease, who had cardiac valvular involvement and severe cardiac disease associated with hepatosplenomegaly.

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

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001366383.2

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

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS3,PS4,PM2,PM3,PP3,PS1_SUP.

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

From Lifecell International Pvt. Ltd, SCV003922073.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Asian1not providednot providedclinical testing PubMed (3)

Description

A Heterozygous Missense variant c.1342G>C in Exon 9 of the GBA1 gene that results in the amino acid substitution p.Asp448His was identified. The observed variant has a minor allele frequency of 0.00013 in gnomAD exomes and is novel in genomes. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic/Likely Pathogenic [Variation ID: 4293]. The observed variant has been previously reported in patients affected with Gaucher disease (Kurolap, Alina et al., 2019). Furthermore, experimental studies have shown that this missense change affects GBA function (Xu, Y H et al., 2011). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 24, 2024