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NM_006493.4(CLN5):c.466C>T (p.Pro156Ser) AND Neuronal ceroid lipofuscinosis

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 23, 2021
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:
RCV001853061.5

Allele description [Variation Report for NM_006493.4(CLN5):c.466C>T (p.Pro156Ser)]

NM_006493.4(CLN5):c.466C>T (p.Pro156Ser)

Gene:
CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q22.3
Genomic location:
Preferred name:
NM_006493.4(CLN5):c.466C>T (p.Pro156Ser)
HGVS:
  • NC_000013.11:g.76996028C>T
  • NG_009064.1:g.9105C>T
  • NM_001366624.2:c.466C>T
  • NM_006493.4:c.466C>TMANE SELECT
  • NP_001353553.1:p.Pro156Ser
  • NP_006484.2:p.Pro156Ser
  • LRG_692t1:c.613C>T
  • LRG_692:g.9105C>T
  • NC_000013.10:g.77570163C>T
  • NM_006493.2:c.613C>T
Protein change:
P156S
Links:
dbSNP: rs386833977
NCBI 1000 Genomes Browser:
rs386833977
Molecular consequence:
  • NM_001366624.2:c.466C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006493.4:c.466C>T - missense variant - [Sequence Ontology: SO:0001583]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002135790Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 23, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Neuronal ceroid lipofuscinosis in Qatar: report of a novel mutation in ceroid-lipofuscinosis, neuronal 5 in the Arab population.

Al-Kowari MK, Hassan S, El-Said MF, Ben-Omran T, Hedin L, Mole SE, Badii R.

J Child Neurol. 2011 May;26(5):625-9. doi: 10.1177/0883073810387298. Epub 2011 Mar 29.

PubMed [citation]
PMID:
21447811

Update of the mutation spectrum and clinical correlations of over 360 mutations in eight genes that underlie the neuronal ceroid lipofuscinoses.

Kousi M, Lehesjoki AE, Mole SE.

Hum Mutat. 2012 Jan;33(1):42-63. doi: 10.1002/humu.21624. Epub 2011 Nov 16. Review.

PubMed [citation]
PMID:
21990111
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002135790.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individual(s) with neuronal ceroid lipofuscinosis (PMID: 21447811, 21990111). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 56541). This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with serine at codon 205 of the CLN5 protein (p.Pro205Ser). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and serine.

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

Last Updated: Sep 29, 2024