NM_006493.4(CLN5):c.956_959del (p.Lys319fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 17, 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:: RCV001664236.2

Allele description [Variation Report for NM_006493.4(CLN5):c.956_959del (p.Lys319fs)]

NM_006493.4(CLN5):c.956_959del (p.Lys319fs)

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.956_959del (p.Lys319fs)

HGVS:

NC_000013.11:g.77000848_77000851del
NG_009064.1:g.13925_13928del
NM_001366624.2:c.*405_*408del
NM_006493.4:c.956_959delMANE SELECT
NP_006484.2:p.Lys319fs
LRG_692t1:c.1103_1106del
LRG_692:g.13925_13928del
NC_000013.10:g.77574980_77574983del
NC_000013.10:g.77574983_77574986del
NM_006493.2:c.1103_1106del
NM_006493.2:c.1103_1106delAACA
NM_006493.4:c.956_959delAACAMANE SELECT

Protein change:

K319fs

Links:

dbSNP: rs386833967

NCBI 1000 Genomes Browser:

rs386833967

Molecular consequence:

NM_001366624.2:c.*405_*408del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_006493.4:c.956_959del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Vaccination
Vaccination
Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis.<br/>

MeSH

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001874845	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 17, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001874845

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 17, 2021)

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, SCV001874845.1

#	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 protein truncation, as the last 40 amino acids are replaced with 14 different amino acids, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (Stenson et al., 2014); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31105743, 20157158, 32983231, 21990111, 22532218, 20960652)

#	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

ClinVar

Relating variation to medicine