NM_020738.4(KIDINS220):c.578_579delinsTT (p.Gly193Val) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 13, 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:: RCV001859319.5

Allele description [Variation Report for NM_020738.4(KIDINS220):c.578_579delinsTT (p.Gly193Val)]

NM_020738.4(KIDINS220):c.578_579delinsTT (p.Gly193Val)

Gene:

KIDINS220:kinase D interacting substrate 220 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

2p25.1

Genomic location:

Preferred name:

NM_020738.4(KIDINS220):c.578_579delinsTT (p.Gly193Val)

HGVS:

NC_000002.12:g.8806295_8806296delinsAA
NG_053168.1:g.36344_36345delinsTT
NM_001348729.2:c.581_582delinsTT
NM_001348731.2:c.581_582delinsTT
NM_001348732.2:c.578_579delinsTT
NM_001348734.2:c.581_582delinsTT
NM_001348735.2:c.578_579delinsTT
NM_001348736.2:c.452_453delinsTT
NM_001348738.2:c.578_579delinsTT
NM_001348739.2:c.581_582delinsTT
NM_001348740.2:c.581_582delinsTT
NM_001348741.2:c.578_579delinsTT
NM_001348742.2:c.578_579delinsTT
NM_001348743.2:c.578_579delinsTT
NM_001348745.2:c.581_582delinsTT
NM_020738.2:c.578_579delinsTT
NM_020738.4:c.578_579delinsTTMANE SELECT
NP_001335658.1:p.Gly194Val
NP_001335660.1:p.Gly194Val
NP_001335661.1:p.Gly193Val
NP_001335663.1:p.Gly194Val
NP_001335664.1:p.Gly193Val
NP_001335665.1:p.Gly151Val
NP_001335667.1:p.Gly193Val
NP_001335668.1:p.Gly194Val
NP_001335669.1:p.Gly194Val
NP_001335670.1:p.Gly193Val
NP_001335671.1:p.Gly193Val
NP_001335672.1:p.Gly193Val
NP_001335674.1:p.Gly194Val
NP_065789.1:p.Gly193Val
NC_000002.11:g.8946425_8946426delinsAA
NM_020738.3:c.578_579delinsTT
NR_145964.2:n.751_752delinsTT
NR_145965.2:n.748_749delinsTT

Protein change:

G151V

Links:

dbSNP: rs1675445207

NCBI 1000 Genomes Browser:

rs1675445207

Molecular consequence:

NM_001348729.2:c.581_582delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348731.2:c.581_582delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348732.2:c.578_579delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348734.2:c.581_582delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348735.2:c.578_579delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348736.2:c.452_453delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348738.2:c.578_579delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348739.2:c.581_582delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348740.2:c.581_582delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348741.2:c.578_579delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348742.2:c.578_579delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348743.2:c.578_579delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001348745.2:c.581_582delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_020738.4:c.578_579delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NR_145964.2:n.751_752delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_145965.2:n.748_749delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Mus musculus ubiquitin specific peptidase 47 (Usp47), transcript variant 2, mRNA
Mus musculus ubiquitin specific peptidase 47 (Usp47), transcript variant 2, mRNA
gi|2214681071|ref|NM_133758.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002249628	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 13, 2021)	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

SCV002249628

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 13, 2021)

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, SCV002249628.2

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

Description

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. 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: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). This variant has been observed in individual(s) with clinical features of hereditary spastic paraplegia (Invitae). ClinVar contains an entry for this variant (Variation ID: 1032095). The frequency data for this variant in the population databases is not available, as this variant may be reported as separate entries in the ExAC database. This sequence change replaces glycine with valine at codon 193 of the KIDINS220 protein (p.Gly193Val). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and valine.

#	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: Oct 8, 2024

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