VCV002930403.2 - ClinVar

NM_017777.4(MKS1):c.633del (p.Tyr213fs)

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.

(2)

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.

Pathogenic/Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_017777.4(MKS1):c.633del (p.Tyr213fs)

Variation ID: 2930403 Accession: VCV002930403.2

Type and length

Deletion, 1 bp

Location

Cytogenetic: 17q22 17: 58214270 (GRCh38) [ NCBI UCSC ] 17: 56291631 (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 29, 2024	Jun 17, 2024	Mar 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_017777.4:c.633del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_060247.2:p.Tyr213fs	frameshift
NM_001321268.2:c.24del	NP_001308197.1:p.Tyr10fs	frameshift
NM_001321269.2:c.633del	NP_001308198.1:p.Tyr213fs	frameshift
NM_001330397.2:c.633del	NP_001317326.1:p.Tyr213fs	frameshift
NM_001411113.1:c.633del	NP_001398042.1:p.Tyr213fs	frameshift
NC_000017.11:g.58214273del
NC_000017.10:g.56291634del
NG_013032.1:g.10336del
LRG_687:g.10336del
LRG_687t1:c.630del	LRG_687p1:p.Tyr213Ilefs

... more HGVS ... less HGVS

Protein change

Y213fs, Y10fs

Other names

Canonical SPDI

NC_000017.11:58214269:CCCC:CCC

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.
MKS1		-	-	GRCh38 GRCh37	980	1067

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.
Familial aplasia of the vermis Meckel-Gruber syndrome	Pathogenic (1)	criteria provided, single submitter	Apr 7, 2023	RCV003789713.2
Bardet-Biedl syndrome 13	Likely pathogenic (1)	criteria provided, single submitter	Mar 20, 2024	RCV004573316.1

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.
Pathogenic (Apr 07, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Familial aplasia of the vermis Meckel-Gruber syndrome 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	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004575851.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Publications: PubMed (3) PubMed: 19466712‚ 24886560‚ 26490104 Comment: This variant has not been reported in the literature in individuals affected with MKS1-related conditions. This variant is present in population databases (no rsID available, … (more) This variant has not been reported in the literature in individuals affected with MKS1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Tyr213Ilefs*16) in the MKS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MKS1 are known to be pathogenic (PMID: 19466712, 24886560, 26490104). For these reasons, this variant has been classified as Pathogenic. (less)
Likely pathogenic (Mar 20, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Bardet-Biedl syndrome 13 Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV005057924.1 First in ClinVar: Jun 17, 2024 Last updated: Jun 17, 2024

Comment:

This variant has not been reported in the literature in individuals affected with MKS1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Tyr213Ilefs*16) in the MKS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MKS1 are known to be pathogenic (PMID: 19466712, 24886560, 26490104). For these reasons, this variant has been classified as Pathogenic.

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

Title	Author	Journal	Year	Link
MKS1 regulates ciliary INPP5E levels in Joubert syndrome.	Slaats GG	Journal of medical genetics	2016	PMID: 26490104
Mutations in B9D1 and MKS1 cause mild Joubert syndrome: expanding the genetic overlap with the lethal ciliopathy Meckel syndrome.	Romani M	Orphanet journal of rare diseases	2014	PMID: 24886560
Mutation spectrum of Meckel syndrome genes: one group of syndromes or several distinct groups?	Tallila J	Human mutation	2009	PMID: 19466712

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_017777.4(MKS1):c.633del (p.Tyr213fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...