NM_024301.5(FKRP):c.1387A>G (p.Asn463Asp) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jan 25, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000178346.21

Allele description [Variation Report for NM_024301.5(FKRP):c.1387A>G (p.Asn463Asp)]

NM_024301.5(FKRP):c.1387A>G (p.Asn463Asp)

Gene:

FKRP:fukutin related protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.32

Genomic location:

Preferred name:

NM_024301.5(FKRP):c.1387A>G (p.Asn463Asp)

HGVS:

NC_000019.10:g.46756837A>G
NG_008898.2:g.15792A>G
NM_001039885.3:c.1387A>G
NM_024301.5:c.1387A>GMANE SELECT
NP_001034974.1:p.Asn463Asp
NP_077277.1:p.Asn463Asp
NP_077277.1:p.Asn463Asp
LRG_761t1:c.1387A>G
LRG_761:g.15792A>G
LRG_761p1:p.Asn463Asp
NC_000019.9:g.47260094A>G
NM_024301.4:c.1387A>G
NM_024301.5(FKRP):c.1387A>GMANE SELECT
Q9H9S5:p.Asn463Asp

Protein change:

N463D; ASN463ASP

Links:

UniProtKB: Q9H9S5#VAR_065063; OMIM: 606596.0018; dbSNP: rs121908110

NCBI 1000 Genomes Browser:

rs121908110

Molecular consequence:

NM_001039885.3:c.1387A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_024301.5:c.1387A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Euphorbia peplus geranylgeranyl diphosphate synthase 1 mRNA, complete cds
Euphorbia peplus geranylgeranyl diphosphate synthase 1 mRNA, complete cds
gi|1545819528|gb|MH363711.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000230411	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Jun 30, 2016)	germline	clinical testing	Citation Link,
SCV001765021	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Dec 3, 2021)	germline	clinical testing	Citation Link,
SCV002017776	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 25, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000230411

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Pathogenic
(Jun 30, 2016)

germline

clinical testing

Citation Link,

SCV001765021

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Dec 3, 2021)

germline

clinical testing

Citation Link,

SCV002017776

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 25, 2023)

germline

clinical testing

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	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	7	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Eurofins Ntd Llc (ga), SCV000230411.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	7	not provided	not provided	clinical testing	not provided

#	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		7	not provided	not provided	not provided

From GeneDx, SCV001765021.3

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

Description

Published functional study demonstrates c.1387A>G showed significantly decreased to absent glycosylated alpha-DG positivity with IIH6 antibody, and mild, variable decreases in beta-DG, dystrophin, and merosin (Lee et al., 2019); Reported in ClinVar but additional evidence is not available (ClinVar Variant ID 4235; ClinVar); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31041397, 17336067, 29065428, 31980526)

#	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

From Revvity Omics, Revvity, SCV002017776.3

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

#	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

Last Updated: Nov 10, 2024

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