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NM_001909.5(CTSD):c.299C>T (p.Ser100Phe) AND Inborn genetic diseases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 26, 2018
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:
RCV002433840.2

Allele description [Variation Report for NM_001909.5(CTSD):c.299C>T (p.Ser100Phe)]

NM_001909.5(CTSD):c.299C>T (p.Ser100Phe)

Gene:
CTSD:cathepsin D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.5
Genomic location:
Preferred name:
NM_001909.5(CTSD):c.299C>T (p.Ser100Phe)
Other names:
p.S100F:TCC>TTC
HGVS:
  • NC_000011.10:g.1759569G>A
  • NG_008655.1:g.9424C>T
  • NM_001909.5:c.299C>TMANE SELECT
  • NP_001900.1:p.Ser100Phe
  • NC_000011.9:g.1780799G>A
  • NM_001909.4:c.299C>T
Protein change:
S100F
Links:
dbSNP: rs796052407
NCBI 1000 Genomes Browser:
rs796052407
Molecular consequence:
  • NM_001909.5:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002746970Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Jan 26, 2018) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Novel mutation and the first prenatal screening of cathepsin D deficiency (CLN10).

Fritchie K, Siintola E, Armao D, Lehesjoki AE, Marino T, Powell C, Tennison M, Booker JM, Koch S, Partanen S, Suzuki K, Tyynelä J, Thorne LB.

Acta Neuropathol. 2009 Feb;117(2):201-8. doi: 10.1007/s00401-008-0426-7. Epub 2008 Sep 2.

PubMed [citation]
PMID:
18762956

Details of each submission

From Ambry Genetics, SCV002746970.2

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

Description

The p.S100F variant (also known as c.299C>T), located in coding exon 3 of the CTSD gene, results from a C to T substitution at nucleotide position 299. The serine at codon 100 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This alteration was detected in the homozygous state in an individual with congenital neuronal ceroid lipofuscinosis (NCL). In addition, authors found very low enzyme activity in this individual's fibroblasts as well as reduced CTSD activity in functional studies (Fritchie K et al. Acta Neuropathol., 2009 Feb;117:201-8). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: May 16, 2025