VCV002388181.7 - ClinVar

NM_020738.4(KIDINS220):c.517C>T (p.Pro173Ser)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(4)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Uncertain significance(2); Likely benign(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_020738.4(KIDINS220):c.517C>T (p.Pro173Ser)

Variation ID: 2388181 Accession: VCV002388181.7

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 2p25.1 2: 8806357 (GRCh38) [ NCBI UCSC ] 2: 8946487 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 8, 2023	Oct 8, 2024	Oct 7, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_020738.4:c.517C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_065789.1:p.Pro173Ser	missense
NM_001348729.2:c.520C>T	NP_001335658.1:p.Pro174Ser	missense
NM_001348731.2:c.520C>T	NP_001335660.1:p.Pro174Ser	missense
NM_001348732.1:c.517C>T
NM_001348732.2:c.517C>T	NP_001335661.1:p.Pro173Ser	missense
NM_001348734.2:c.520C>T	NP_001335663.1:p.Pro174Ser	missense
NM_001348735.2:c.517C>T	NP_001335664.1:p.Pro173Ser	missense
NM_001348736.2:c.391C>T	NP_001335665.1:p.Pro131Ser	missense
NM_001348738.2:c.517C>T	NP_001335667.1:p.Pro173Ser	missense
NM_001348739.2:c.520C>T	NP_001335668.1:p.Pro174Ser	missense
NM_001348740.2:c.520C>T	NP_001335669.1:p.Pro174Ser	missense
NM_001348741.2:c.517C>T	NP_001335670.1:p.Pro173Ser	missense
NM_001348742.2:c.517C>T	NP_001335671.1:p.Pro173Ser	missense
NM_001348743.2:c.517C>T	NP_001335672.1:p.Pro173Ser	missense
NM_001348745.2:c.520C>T	NP_001335674.1:p.Pro174Ser	missense
NR_145964.2:n.690C>T		non-coding transcript variant
NR_145965.2:n.687C>T		non-coding transcript variant
NC_000002.12:g.8806357G>A
NC_000002.11:g.8946487G>A
NG_053168.1:g.36283C>T
NG_053168.2:g.36256C>T

... more HGVS ... less HGVS

Protein change

P131S, P173S, P174S

Other names

Canonical SPDI

NC_000002.12:8806356:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
KIDINS220		-	-	GRCh38 GRCh37	945	969

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Inborn genetic diseases	Likely benign (1)	criteria provided, single submitter	Dec 1, 2022	RCV002698838.2
Spastic paraplegia, intellectual disability, nystagmus, and obesity Ventriculomegaly and arthrogryposis	Uncertain significance (1)	criteria provided, single submitter	Sep 30, 2022	RCV003228136.2
not provided	Uncertain significance (1)	criteria provided, single submitter	Oct 7, 2023	RCV003561166.3
KIDINS220-related disorder	Uncertain significance (1)	no assertion criteria provided	Apr 25, 2024	RCV003918993.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Sep 30, 2022)	criteria provided, single submitter (NYGC Assertion Criteria 2020) Method: clinical testing	Spastic paraplegia, intellectual disability, nystagmus, and obesity Ventriculomegaly and arthrogryposis Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	New York Genome Center Accession: SCV003925142.2 First in ClinVar: May 20, 2023 Last updated: Oct 21, 2023	Observation 1: Clinical Features: Diabetes mellitus (present) Secondary finding: no Observation 2: Number of individuals with the variant: 1 Clinical Features: Hyperlipidemia (present) , Type 2 diabetes mellitus (present) Secondary finding: no
Uncertain significance (Oct 07, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004285774.1 First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024	Comment: This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 173 of the KIDINS220 protein (p.Pro173Ser). … (more) This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 173 of the KIDINS220 protein (p.Pro173Ser). This variant is present in population databases (rs374716369, gnomAD 0.1%). 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: 2388181). 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. (less)
Likely benign (Dec 01, 2022)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV003726928.2 First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024	Comment: This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more) This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
Uncertain significance (Apr 25, 2024)	no assertion criteria provided Method: clinical testing	KIDINS220-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004736970.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: The KIDINS220 c.517C>T variant is predicted to result in the amino acid substitution p.Pro173Ser. To our knowledge, this variant has not been reported in the … (more) The KIDINS220 c.517C>T variant is predicted to result in the amino acid substitution p.Pro173Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.091% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)

Comment:

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 173 of the KIDINS220 protein (p.Pro173Ser). This variant is present in population databases (rs374716369, gnomAD 0.1%). 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: 2388181). 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.

Comment:

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Comment:

The KIDINS220 c.517C>T variant is predicted to result in the amino acid substitution p.Pro173Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.091% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Germline Functional Evidence

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.

Comment:

Citations for germline classification of this variant

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

Text-mined citations for this variant ...

Record last updated Oct 13, 2024

ClinVar Genomic variation as it relates to human health

NM_020738.4(KIDINS220):c.517C>T (p.Pro173Ser)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...