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NM_006846.3(SPINK5):c.2468del (p.Lys823fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Sep 24, 2021)
Last evaluated:
May 11, 2020
Accession:
VCV000523932.4
Variation ID:
523932
Description:
1bp deletion
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NM_006846.3(SPINK5):c.2468del (p.Lys823fs)

Allele ID
514505
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
5q32
Genomic location
5: 148120312 (GRCh38) GRCh38 UCSC
5: 147499875 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_110:g.61350del
LRG_110t1:c.2468del LRG_110p1:p.Lys823fs
NM_006846.3:c.2468delA frameshift
... more HGVS
Protein change
K823fs
Other names
-
Canonical SPDI
NC_000005.10:148120311:AAAAAAAAAA:AAAAAAAAA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA3496004
dbSNP: rs565782662
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter May 11, 2020 RCV000627412.2
Pathogenic 1 no assertion criteria provided Jan 6, 2020 RCV000991162.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPINK5 - - GRCh38
GRCh37
601 618

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 11, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000748407.3
Submitted: (Sep 24, 2021)
Evidence details
Comment:
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 … (more)
Pathogenic
(Jan 06, 2020)
no assertion criteria provided
Method: curation
Netherton syndrome
Allele origin: germline
Reproductive Health Research and Development,BGI Genomics
Accession: SCV001142348.1
Submitted: (Jan 06, 2020)
Evidence details
Comment:
NM_006846.3:c.2468delA in the SPINK5 gene has an allele frequency of 0.005 in South subpopulation in the gnomAD database. This variant has been reported previously in … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs565782662...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 26, 2021