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NM_000391.4(TPP1):c.1340G>A (p.Arg447His) AND Neuronal ceroid lipofuscinosis 2

Germline classification:
Pathogenic/Likely pathogenic (6 submissions)
Last evaluated:
Apr 4, 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:
RCV000002764.12

Allele description

NM_000391.4(TPP1):c.1340G>A (p.Arg447His)

Gene:
TPP1:tripeptidyl peptidase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_000391.4(TPP1):c.1340G>A (p.Arg447His)
Other names:
5457G>A; p.R447H:CGT>CAT
HGVS:
  • NC_000011.10:g.6615256C>T
  • NG_008653.1:g.9206G>A
  • NM_000391.4:c.1340G>AMANE SELECT
  • NP_000382.3:p.Arg447His
  • LRG_830t1:c.1340G>A
  • LRG_830:g.9206G>A
  • LRG_830p1:p.Arg447His
  • NC_000011.9:g.6636487C>T
  • NM_000391.3:c.1340G>A
  • O14773:p.Arg447His
Protein change:
R447H; ARG447HIS
Links:
UniProtKB: O14773#VAR_005645; UniProtKB/Swiss-Prot: VAR_005645; OMIM: 607998.0005; dbSNP: rs119455956
NCBI 1000 Genomes Browser:
rs119455956
Molecular consequence:
  • NM_000391.4:c.1340G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Neuronal ceroid lipofuscinosis 2
Synonyms:
JANSKY-BIELSCHOWSKY DISEASE NEURONAL CEROID LIPOFUSCINOSIS, LATE INFANTILE; TPP1-Related Neuronal Ceroid-Lipofuscinosis
Identifiers:
MONDO: MONDO:0008769; MedGen: C1876161; Orphanet: 168491; Orphanet: 228349; Orphanet: 79264; OMIM: 204500

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000022922OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 1999)
germlineliterature only

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

SCV000091187UniProtKB/Swiss-Prot
no classification provided
not providednot providednot provided

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

SCV000746792Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 18, 2017)
inheritedclinical testing

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

SCV002060995Medical Genetic Institute of Henan Province, Henan Provincial People’s Hospital
no assertion criteria provided
Pathogenicbiparentalcase-control

SCV002094812Natera, Inc.
no assertion criteria provided
Pathogenic
(Jan 25, 2021)
germlineclinical testing

SCV004809407Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Apr 4, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedbiparentalunknownnot providednot providednot providednot providednot providedcase-control
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providednot providednot providednot providednot providednot provided1not providedliterature only
not providedinheritedyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutational analysis of the defective protease in classic late-infantile neuronal ceroid lipofuscinosis, a neurodegenerative lysosomal storage disorder.

Sleat DE, Gin RM, Sohar I, Wisniewski K, Sklower-Brooks S, Pullarkat RK, Palmer DN, Lerner TJ, Boustany RM, Uldall P, Siakotos AN, Donnelly RJ, Lobel P.

Am J Hum Genet. 1999 Jun;64(6):1511-23. Erratum in: Am J Hum Genet. 2004 Dec;75(6):1158.

PubMed [citation]
PMID:
10330339
PMCID:
PMC1377895

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From OMIM, SCV000022922.2

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

Description

In 2 unrelated patients with juvenile-onset neuronal ceroid lipofuscinosis-2 (CLN2; 204500), Sleat et al. (1999) identified a rare monoallelic mutation that resulted in an arg447-to-his (R447H) substitution in the CLN2 gene. Both of these patients were compound heterozygous, with either a monoallelic common splice junction mutation (607998.0004) or the arg208-to-ter mutation (R208X; 607998.0003). Both patients were originally diagnosed with juvenile-onset CLN3 (204200) on the basis of age at onset, age at death, and inclusion morphology. Sleat et al. (1999) considered it likely that the R447H mutation caused incomplete loss of function of the CLN2 protease, resulting in the protracted phenotype. The findings indicated that an attenuated form of CLN2 (i.e., with juvenile onset) may not be correctly diagnosed or may be confused with other later-onset neurodegenerative disorders. Such observations are not uncommon with other lysosomal storage diseases, in which missense mutations result in a partial dysfunction and subsequent mild or protracted phenotype. The possible phenotype of an individual homozygous for the R447H allele remained unknown.

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

From UniProtKB/Swiss-Prot, SCV000091187.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000746792.2

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

From Medical Genetic Institute of Henan Province, Henan Provincial People’s Hospital, SCV002060995.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedcase-controlnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1biparentalunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV002094812.1

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

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004809407.1

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

Last Updated: Jun 23, 2024