NM_006493.4(CLN5):c.777_778del (p.Phe260fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 19, 2024
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:: RCV000413943.5

Allele description [Variation Report for NM_006493.4(CLN5):c.777_778del (p.Phe260fs)]

NM_006493.4(CLN5):c.777_778del (p.Phe260fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

13q22.3

Genomic location:

Preferred name:

NM_006493.4(CLN5):c.777_778del (p.Phe260fs)

HGVS:

NC_000013.11:g.77000667AT[1]
NG_009064.1:g.13744AT[1]
NM_001366624.2:c.*224AT[1]
NM_006493.4:c.777_778delMANE SELECT
NP_006484.2:p.Phe260fs
LRG_692t1:c.924_925del
LRG_692:g.13744AT[1]
NC_000013.10:g.77574802AT[1]
NC_000013.10:g.77574802_77574803del
NM_006493.2:c.924_925del
NM_006493.2:c.924_925delAT

Protein change:

F260fs

Links:

dbSNP: rs786204644

NCBI 1000 Genomes Browser:

rs786204644

Molecular consequence:

NM_001366624.2:c.*224AT[1] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_006493.4:c.777_778del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000491175	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jul 19, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000491175

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jul 19, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000491175.5

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

Description

Frameshift variant predicted to result in abnormal protein length as the last 99 amino acids are replaced with 11 different amino acids, and other similar variants have been reported in HGMD; This variant is associated with the following publications: (PMID: 22532218, 31440721, 20157158)

#	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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