VCV000459226.8 - ClinVar

NM_024301.5(FKRP):c.1019A>T (p.Tyr340Phe)

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.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_024301.5(FKRP):c.1019A>T (p.Tyr340Phe)

Variation ID: 459226 Accession: VCV000459226.8

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 19q13.32 19: 46756469 (GRCh38) [ NCBI UCSC ] 19: 47259726 (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	Aug 11, 2024	Mar 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_024301.5:c.1019A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_077277.1:p.Tyr340Phe	missense
NM_001039885.3:c.1019A>T	NP_001034974.1:p.Tyr340Phe	missense
NC_000019.10:g.46756469A>T
NC_000019.9:g.47259726A>T
NG_008898.2:g.15424A>T
LRG_761:g.15424A>T
LRG_761t1:c.1019A>T	LRG_761p1:p.Tyr340Phe

... more HGVS ... less HGVS

Protein change

Y340F

Other names

Canonical SPDI

NC_000019.10:46756468:A:T

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.

The Genome Aggregation Database (gnomAD) 0.00001

Trans-Omics for Precision Medicine (TOPMed) 0.00001

Links

ClinGen: CA406496482 dbSNP: rs1322997651 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.
FKRP		-	-	GRCh38 GRCh37	1056	1100

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.
Walker-Warburg congenital muscular dystrophy	Uncertain significance (1)	criteria provided, single submitter	Nov 21, 2021	RCV000538732.4
Autosomal recessive limb-girdle muscular dystrophy type 2I Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5 Muscular dystrophy-dystroglycanopathy type B5	Uncertain significance (1)	criteria provided, single submitter	Oct 31, 2018	RCV000765455.2
Cardiovascular phenotype	Uncertain significance (1)	criteria provided, single submitter	Mar 20, 2024	RCV003302800.3
Autosomal recessive limb-girdle muscular dystrophy type 2I	Uncertain significance (1)	no assertion criteria provided	Sep 16, 2020	RCV001273520.1

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.
Uncertain significance (Oct 31, 2018)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 Muscular dystrophy-dystroglycanopathy type B5 Autosomal recessive limb-girdle muscular dystrophy type 2I Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV000896746.1 First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019	Publications: PubMed (1) PubMed: 25741868 pmc: 4544753 pmc: 4544753 DOI: 10.1038/gim.2015.30 DOI: 10.1038/gim.2015.30
Uncertain significance (Nov 21, 2021)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Walker-Warburg congenital muscular dystrophy Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000630826.3 First in ClinVar: Dec 26, 2017 Last updated: Feb 07, 2023	Comment: This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 340 of the FKRP protein (p.Tyr340Phe). … (more) This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 340 of the FKRP protein (p.Tyr340Phe). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FKRP-related conditions. ClinVar contains an entry for this variant (Variation ID: 459226). 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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)
Uncertain significance (Mar 20, 2024)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Cardiovascular phenotype Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV004003023.3 First in ClinVar: Jul 08, 2023 Last updated: Aug 11, 2024	Comment: The c.1019A>T (p.Y340F) alteration is located in exon 4 (coding exon 1) of the FKRP gene. This alteration results from a A to T substitution … (more) The c.1019A>T (p.Y340F) alteration is located in exon 4 (coding exon 1) of the FKRP gene. This alteration results from a A to T substitution at nucleotide position 1019, causing the tyrosine (Y) at amino acid position 340 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
Uncertain significance (Sep 16, 2020)	no assertion criteria provided Method: clinical testing	Limb-girdle muscular dystrophy type 2I Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV001456657.1 First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021

Comment:

This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 340 of the FKRP protein (p.Tyr340Phe). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FKRP-related conditions. ClinVar contains an entry for this variant (Variation ID: 459226). 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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:

The c.1019A>T (p.Y340F) alteration is located in exon 4 (coding exon 1) of the FKRP gene. This alteration results from a A to T substitution at nucleotide position 1019, causing the tyrosine (Y) at amino acid position 340 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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 rs1322997651 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_024301.5(FKRP):c.1019A>T (p.Tyr340Phe)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1322997651 ...