NM_020738.4(KIDINS220):c.2569G>A (p.Val857Ile) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Dec 11, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV002032238.17

Allele description [Variation Report for NM_020738.4(KIDINS220):c.2569G>A (p.Val857Ile)]

NM_020738.4(KIDINS220):c.2569G>A (p.Val857Ile)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

2p25.1

Genomic location:

Preferred name:

NM_020738.4(KIDINS220):c.2569G>A (p.Val857Ile)

HGVS:

NC_000002.12:g.8778941C>T
NG_053168.1:g.63699G>A
NM_001348729.2:c.2572G>A
NM_001348731.2:c.2572G>A
NM_001348732.2:c.2569G>A
NM_001348734.2:c.2572G>A
NM_001348735.2:c.2569G>A
NM_001348736.2:c.2443G>A
NM_001348738.2:c.2569G>A
NM_001348739.2:c.2572G>A
NM_001348740.2:c.2572G>A
NM_001348741.2:c.2569G>A
NM_001348742.2:c.2569G>A
NM_001348743.2:c.2569G>A
NM_001348745.2:c.2572G>A
NM_020738.2:c.2569G>A
NM_020738.4:c.2569G>AMANE SELECT
NP_001335658.1:p.Val858Ile
NP_001335660.1:p.Val858Ile
NP_001335661.1:p.Val857Ile
NP_001335663.1:p.Val858Ile
NP_001335664.1:p.Val857Ile
NP_001335665.1:p.Val815Ile
NP_001335667.1:p.Val857Ile
NP_001335668.1:p.Val858Ile
NP_001335669.1:p.Val858Ile
NP_001335670.1:p.Val857Ile
NP_001335671.1:p.Val857Ile
NP_001335672.1:p.Val857Ile
NP_001335674.1:p.Val858Ile
NP_065789.1:p.Val857Ile
NC_000002.11:g.8919071C>T
NR_145964.2:n.2742G>A
NR_145965.2:n.2739G>A

Protein change:

V815I

Links:

dbSNP: rs200104720

NCBI 1000 Genomes Browser:

rs200104720

Molecular consequence:

NM_001348729.2:c.2572G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348731.2:c.2572G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348732.2:c.2569G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348734.2:c.2572G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348735.2:c.2569G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348736.2:c.2443G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348738.2:c.2569G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348739.2:c.2572G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348740.2:c.2572G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348741.2:c.2569G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348742.2:c.2569G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348743.2:c.2569G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348745.2:c.2572G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020738.4:c.2569G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_145964.2:n.2742G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_145965.2:n.2739G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus chromosome 7, clone RP23-103E11, complete sequence
Mus musculus chromosome 7, clone RP23-103E11, complete sequence
gi|32996835|gnl|WIBR|L8059|gb|AC026 1|

Nucleotide
K Homology domain-containing protein [Caenorhabditis elegans]
K Homology domain-containing protein [Caenorhabditis elegans]
gi|71986869|ref|NP_490681.2|

Protein
Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clo...
Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clone:I1C0019G20 product:ribonuclease/angiogenin inhibitor 2, full insert sequence
gi|74184927|dbj|AK166869.1|

Nucleotide
Solanum habrochaites voucher LA2175A self-incompatibility ribonuclease (SRN) gen...
Solanum habrochaites voucher LA2175A self-incompatibility ribonuclease (SRN) gene, SRN-hab-15 allele, complete cds
gi|2286540102|gb|OK091164.1|

Nucleotide
Solanum lycopersicum chloroplast, complete genome
Solanum lycopersicum chloroplast, complete genome
gi|2496525246|gb|OQ473549.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002313379	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004138564	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2022)	germline	clinical testing	Citation Link,
SCV005186420	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002313379

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 2023)

germline

clinical testing

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

SCV004138564

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Jul 1, 2022)

germline

clinical testing

Citation Link,

SCV005186420

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

not provided

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	yes	1	not provided	not provided	not provided	not provided	clinical testing, not provided
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002313379.3

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

Description

This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 857 of the KIDINS220 protein (p.Val857Ile). This variant is present in population databases (rs200104720, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with KIDINS220-related conditions. ClinVar contains an entry for this variant (Variation ID: 1525138). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. 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.

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004138564.10

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

Description

KIDINS220: BP4

#	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		1	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005186420.1

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

#	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: Oct 20, 2024

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