NM_006493.4(CLN5):c.808_823del (p.Gly270fs) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jan 31, 2022
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:: RCV000675522.9

Allele description [Variation Report for NM_006493.4(CLN5):c.808_823del (p.Gly270fs)]

NM_006493.4(CLN5):c.808_823del (p.Gly270fs)

Gene:

CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q22.3

Genomic location:

Preferred name:

NM_006493.4(CLN5):c.808_823del (p.Gly270fs)

HGVS:

NC_000013.11:g.77000700_77000715del
NG_009064.1:g.13777_13792del
NM_001366624.2:c.*257_*272del
NM_006493.4:c.808_823delMANE SELECT
NP_006484.2:p.Gly270fs
LRG_692t1:c.955_970del
LRG_692:g.13777_13792del
NC_000013.10:g.77574830_77574845del
NC_000013.10:g.77574835_77574850del
NM_006493.2:c.955_970del
NM_006493.2:c.955_970delGGAAATGAAACATCTG
NM_006493.4:c.808_823del16MANE SELECT

Protein change:

G270fs

Links:

dbSNP: rs386833983

NCBI 1000 Genomes Browser:

rs386833983

Molecular consequence:

NM_001366624.2:c.*257_*272del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_006493.4:c.808_823del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000230322	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Nov 8, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000801213	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Likely pathogenic (Jun 1, 2017)	unknown	clinical testing
SCV002558287	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jan 31, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000230322

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Nov 8, 2014)

germline

clinical testing

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

Citation Link,

SCV000801213

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Likely pathogenic
(Jun 1, 2017)

unknown

clinical testing

SCV002558287

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jan 31, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	3	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Details of each submission

From Eurofins Ntd Llc (ga), SCV000230322.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	PubMed (1)

#	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		3	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801213.1

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

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

From GeneDx, SCV002558287.2

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

Description

Identified with a second CLN5 variant in an individual with neuronal ceroid lipofuscinoses, however, clinical and familial segregation information was not provided (Kousi M et al., 2012); Frameshift variant predicted to result in protein truncation, as the last 89 amino acids are replaced with 11 different amino acids, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 21990111)

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

Last Updated: Sep 29, 2024

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