NM_017882.3(CLN6):c.559C>T (p.Leu187Phe) AND Neuronal ceroid lipofuscinosis

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 12, 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:: RCV000815648.7

Allele description [Variation Report for NM_017882.3(CLN6):c.559C>T (p.Leu187Phe)]

NM_017882.3(CLN6):c.559C>T (p.Leu187Phe)

Gene:

CLN6:CLN6 transmembrane ER protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q23

Genomic location:

Preferred name:

NM_017882.3(CLN6):c.559C>T (p.Leu187Phe)

HGVS:

NC_000015.10:g.68209743G>A
NG_008764.2:g.52469C>T
NM_017882.3:c.559C>TMANE SELECT
NP_060352.1:p.Leu187Phe
LRG_832t1:c.559C>T
LRG_832:g.52469C>T
LRG_832p1:p.Leu187Phe
NC_000015.9:g.68502081G>A
NM_017882.2:c.559C>T

Protein change:

L187F

Links:

dbSNP: rs764670832

NCBI 1000 Genomes Browser:

rs764670832

Molecular consequence:

NM_017882.3:c.559C>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

Recent activity

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PREDICTED: Mus musculus interferon induced with helicase C domain 1 (Ifih1), tra...
PREDICTED: Mus musculus interferon induced with helicase C domain 1 (Ifih1), transcript variant X1, mRNA
gi|1907143362|ref|XM_006500187.5|

Nucleotide
Loasa heterophylla, petal tissue, bud stage, sample 2
Loasa heterophylla, petal tissue, bud stage, sample 2

biosample
myb-binding protein 1A isoform 1 [Homo sapiens]
myb-binding protein 1A isoform 1 [Homo sapiens]
gi|157694494|ref|NP_001099008.1|

Protein
Homo sapiens zinc finger protein 76 (ZNF76), transcript variant 1, mRNA
Homo sapiens zinc finger protein 76 (ZNF76), transcript variant 1, mRNA
gi|1519313160|ref|NM_003427.5|

Nucleotide
purF amidophosphoribosyltransferase [Escherichia coli str. K-12 substr. MG1655]
purF amidophosphoribosyltransferase [Escherichia coli str. K-12 substr. MG1655]
Gene ID:946794

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000956109	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 12, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000956109

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 12, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000956109.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant is present in population databases (rs764670832, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CLN6-related conditions. ClinVar contains an entry for this variant (Variation ID: 658763). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 187 of the CLN6 protein (p.Leu187Phe).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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