NM_007254.4(PNKP):c.1409C>T (p.Ser470Phe) AND Developmental and epileptic encephalopathy, 12

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 25, 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:: RCV001348694.7

Allele description [Variation Report for NM_007254.4(PNKP):c.1409C>T (p.Ser470Phe)]

NM_007254.4(PNKP):c.1409C>T (p.Ser470Phe)

Gene:

PNKP:polynucleotide kinase 3'-phosphatase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_007254.4(PNKP):c.1409C>T (p.Ser470Phe)

HGVS:

NC_000019.10:g.49861488G>A
NG_027717.1:g.11078C>T
NG_050666.1:g.17645G>A
NM_007254.4:c.1409C>TMANE SELECT
NP_009185.2:p.Ser470Phe
NC_000019.9:g.50364745G>A

Protein change:

S470F

Links:

dbSNP: rs1231560062

NCBI 1000 Genomes Browser:

rs1231560062

Molecular consequence:

NM_007254.4:c.1409C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 12 (DEE12)
Synonyms:: Early infantile epileptic encephalopathy 12
Identifiers:: MONDO: MONDO:0013389; MedGen: C3150988; OMIM: 613722

Recent activity

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BEL1-like homeodomain protein 2 [Cucurbita moschata]
BEL1-like homeodomain protein 2 [Cucurbita moschata]
gi|1279793121|ref|XP_022949683.1|

Protein
uncharacterized protein LOC103486663 [Cucumis melo]
uncharacterized protein LOC103486663 [Cucumis melo]
gi|659084462|ref|XP_008442900.1|

Protein
uncharacterized protein LOC120090394 isoform X2 [Benincasa hispida]
uncharacterized protein LOC120090394 isoform X2 [Benincasa hispida]
gi|1955829850|ref|XP_038903952.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001543004	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 25, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001543004

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 25, 2020)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001543004.4

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with PNKP-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with phenylalanine at codon 470 of the PNKP protein (p.Ser470Phe). The serine residue is moderately conserved and there is a large physicochemical difference between serine and phenylalanine.

#	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		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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