NM_006846.4(SPINK5):c.2468del (p.Lys823fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 11, 2020
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:: RCV000627412.2

Allele description [Variation Report for NM_006846.4(SPINK5):c.2468del (p.Lys823fs)]

NM_006846.4(SPINK5):c.2468del (p.Lys823fs)

Gene:

SPINK5:serine peptidase inhibitor Kazal type 5 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q32

Genomic location:

Preferred name:

NM_006846.4(SPINK5):c.2468del (p.Lys823fs)

HGVS:

NC_000005.10:g.148120321del
NG_009633.1:g.61350del
NM_001127698.2:c.2468del
NM_001127699.2:c.2468del
NM_006846.4:c.2468delMANE SELECT
NP_001121170.1:p.Lys823fs
NP_001121171.1:p.Lys823fs
NP_006837.2:p.Lys823fs
NP_006837.2:p.Lys823fs
LRG_110t1:c.2468del
LRG_110:g.61350del
LRG_110p1:p.Lys823fs
NC_000005.9:g.147499875del
NC_000005.9:g.147499884del
NM_006846.3:c.2468del
NM_006846.3:c.2468delA

Protein change:

K823fs

Links:

dbSNP: rs565782662

NCBI 1000 Genomes Browser:

rs565782662

Molecular consequence:

NM_001127698.2:c.2468del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127699.2:c.2468del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006846.4:c.2468del - 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
SCV000748407	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 11, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000748407

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(May 11, 2020)

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, SCV000748407.3

#	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 or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 12923596, 27905021, 11841556, 26229701, 31980526)

#	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: Feb 28, 2024

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