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NM_000391.4(TPP1):c.1397_1408delinsGACACCGA (p.Val466fs) AND Neuronal ceroid lipofuscinosis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 16, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001242500.3

Allele description [Variation Report for NM_000391.4(TPP1):c.1397_1408delinsGACACCGA (p.Val466fs)]

NM_000391.4(TPP1):c.1397_1408delinsGACACCGA (p.Val466fs)

Gene:
TPP1:tripeptidyl peptidase 1 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_000391.4(TPP1):c.1397_1408delinsGACACCGA (p.Val466fs)
HGVS:
  • NC_000011.10:g.6615188_6615199delinsTCGGTGTC
  • NG_008653.1:g.9263_9274delinsGACACCGA
  • NM_000391.4:c.1397_1408delinsGACACCGAMANE SELECT
  • NP_000382.3:p.Val466fs
  • LRG_830t1:c.1397_1408delinsGACACCGA
  • LRG_830:g.9263_9274delinsGACACCGA
  • LRG_830p1:p.Val466fs
  • NC_000011.9:g.6636419_6636430delinsTCGGTGTC
  • NC_000011.9:g.6636419_6636430delinsTCGGTGTC
  • NM_000391.3:c.1397_1408delinsGACACCGA
Protein change:
V466fs
Links:
dbSNP: rs1855559514
NCBI 1000 Genomes Browser:
rs1855559514
Molecular consequence:
  • NM_000391.4:c.1397_1408delinsGACACCGA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Neuronal ceroid lipofuscinosis
Synonyms:
Ceroid storage disease
Identifiers:
MONDO: MONDO:0016295; MedGen: C0027877; Orphanet: 79263; OMIM: PS256730

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002819601Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Dec 16, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002819601.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: TPP1 c.1397_1408delinsGACACCGA (p.Val466GlyfsX21) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory and associated with Neuronal Ceroid-Lipofuscinosis in HGMD. The variant was absent in 282854 control chromosomes. To our knowledge, no occurrence of c.1397_1408delinsGACACCGA in individuals affected with Neuronal Ceroid-Lipofuscinosis (Batten Disease) and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessment for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Sep 29, 2024