NM_001370298.3(FGD4):c.2560G>A (p.Val854Met) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(3) (Last evaluated: Oct 23, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
6 submissions [Details]
Record status:
current
Accession:
RCV000727143.11

Allele description [Variation Report for NM_001370298.3(FGD4):c.2560G>A (p.Val854Met)]

NM_001370298.3(FGD4):c.2560G>A (p.Val854Met)

Gene:
FGD4:FYVE, RhoGEF and PH domain containing 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p11.21
Genomic location:
Preferred name:
NM_001370298.3(FGD4):c.2560G>A (p.Val854Met)
HGVS:
  • NC_000012.12:g.32640381G>A
  • NG_008626.2:g.245853G>A
  • NM_001304481.1:c.2404G>A
  • NM_001304484.2:c.1117G>A
  • NM_001330373.2:c.1870G>A
  • NM_001330374.2:c.1870G>A
  • NM_001370297.1:c.1597G>A
  • NM_001370298.3:c.2560G>AMANE SELECT
  • NM_001384126.1:c.2560G>A
  • NM_001384127.1:c.2149G>A
  • NM_001384128.1:c.2149G>A
  • NM_001384130.1:c.1870G>A
  • NM_001385118.1:c.2149G>A
  • NM_139241.3:c.2149G>A
  • NP_001291410.1:p.Val802Met
  • NP_001291413.1:p.Val373Met
  • NP_001317302.1:p.Val624Met
  • NP_001317303.1:p.Val624Met
  • NP_001357226.1:p.Val533Met
  • NP_001357227.2:p.Val854Met
  • NP_001371055.1:p.Val854Met
  • NP_001371056.1:p.Val717Met
  • NP_001371057.1:p.Val717Met
  • NP_001371059.1:p.Val624Met
  • NP_001372047.1:p.Val717Met
  • NP_640334.2:p.Val717Met
  • LRG_240t1:c.2149G>A
  • LRG_240t2:c.2404G>A
  • LRG_240:g.245853G>A
  • LRG_240p1:p.Val717Met
  • LRG_240p2:p.Val802Met
  • NC_000012.11:g.32793315G>A
  • NM_139241.2:c.2149G>A
Protein change:
V373M
Links:
dbSNP: rs61753359
NCBI 1000 Genomes Browser:
rs61753359
Molecular consequence:
  • NM_001304481.1:c.2404G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304484.2:c.1117G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330373.2:c.1870G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330374.2:c.1870G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370297.1:c.1597G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370298.3:c.2560G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384126.1:c.2560G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384127.1:c.2149G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384128.1:c.2149G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384130.1:c.1870G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385118.1:c.2149G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139241.3:c.2149G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
4

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000292552GeneDxcriteria provided, single submitter
Likely benign
(Sep 14, 2020)
germlineclinical testing

Citation Link,

SCV000706120EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Feb 9, 2017)
germlineclinical testing

Citation Link,

SCV000892022CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(May 1, 2019)
germlineclinical testing

Citation Link,

SCV001714405Mayo Clinic Laboratories,Mayo Cliniccriteria provided, single submitter
Uncertain significance
(Oct 23, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001918771Clinical Genetics,Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedUncertain significancegermlineclinical testing

SCV001969891Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedUncertain significancegermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknown2not providednot providednot providednot providedclinical 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 GeneDx, SCV000292552.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is associated with the following publications: (PMID: 21376300, 32376792)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000706120.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV000892022.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Mayo Clinic Laboratories,Mayo Clinic, SCV001714405.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Clinical Genetics,Academic Medical Center - VKGL Data-share Consensus, SCV001918771.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001969891.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 2, 2021

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