VCV000456874.13 - ClinVar

NM_000219.6(KCNE1):c.111_112inv (p.Ser38Gly)

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.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000219.6(KCNE1):c.111_112inv (p.Ser38Gly)

Variation ID: 456874 Accession: VCV000456874.13

Type and length

Inversion, 2 bp

Location

Cytogenetic: 21q22.12 21: 34449523-34449524 (GRCh38) [ NCBI UCSC ] 21: 35821821-35821822 (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	Dec 26, 2017	May 1, 2024	Nov 1, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000219.6:c.111_112delinsTG MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NM_000219.6:c.111_112inv MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000210.2:p.Ser38Gly	missense
NM_000219.5:c.111_112delinsTG
NM_001127668.4:c.111_112inv	NP_001121140.1:p.Ser38Gly	missense
NM_001127669.4:c.111_112inv	NP_001121141.1:p.Ser38Gly	missense
NM_001127670.4:c.111_112inv	NP_001121142.1:p.Ser38Gly	missense
NM_001270402.3:c.111_112inv	NP_001257331.1:p.Ser38Gly	missense
NM_001270403.2:c.111_112inv	NP_001257332.1:p.Ser38Gly	missense
NM_001270404.3:c.111_112inv	NP_001257333.1:p.Ser38Gly	missense
NM_001270405.3:c.111_112inv	NP_001257334.1:p.Ser38Gly	missense
NC_000021.9:g.34449523_34449524inv
NC_000021.8:g.35821821_35821822inv
NG_009091.1:g.66792_66793inv
LRG_290:g.66792_66793inv
LRG_290t1:c.111_112delCAinsTG

... more HGVS ... less HGVS

Protein change

S38G

Other names

Canonical SPDI

NC_000021.9:34449522:TG:CA

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

ClinGen: CA658658886 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.
KCNE1		-	-	GRCh38 GRCh37	341	419

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.
Long QT syndrome	Likely benign (1)	criteria provided, single submitter	Nov 1, 2023	RCV000531649.9
not provided	Benign (1)	criteria provided, single submitter	Aug 21, 2017	RCV001534710.2
Cardiovascular phenotype	Benign (1)	criteria provided, single submitter	Apr 26, 2022	RCV002431536.2
Jervell and Lange-Nielsen syndrome 2 Long QT syndrome 5	Likely benign (1)	criteria provided, single submitter	Nov 17, 2021	RCV002490956.1

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.
Benign (Aug 21, 2017)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001751652.1 First in ClinVar: Jul 18, 2021 Last updated: Jul 18, 2021
Likely benign (Nov 17, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Jervell and Lange-Nielsen syndrome 2 Long QT syndrome 5 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002800409.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022
Likely benign (Nov 01, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Long QT syndrome Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000627405.6 First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024
Benign (Apr 26, 2022)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Cardiovascular phenotype Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV002742713.2 First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024	Comment: This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation … (more) This alteration is classified as 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)

Comment:

This alteration is classified as 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.

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 Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_000219.6(KCNE1):c.111_112inv (p.Ser38Gly)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...