NM_001370298.3(FGD4):c.740T>C (p.Leu247Pro) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Dec 30, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000233379.5

Allele description [Variation Report for NM_001370298.3(FGD4):c.740T>C (p.Leu247Pro)]

NM_001370298.3(FGD4):c.740T>C (p.Leu247Pro)

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.740T>C (p.Leu247Pro)
HGVS:
  • NC_000012.12:g.32582196T>C
  • NG_008626.2:g.187668T>C
  • NM_001304481.1:c.584T>C
  • NM_001304483.2:c.-516T>C
  • NM_001304484.2:c.-823T>C
  • NM_001330373.2:c.50T>C
  • NM_001330374.2:c.50T>C
  • NM_001370297.1:c.49-16301T>C
  • NM_001370298.3:c.740T>CMANE SELECT
  • NM_001384126.1:c.740T>C
  • NM_001384127.1:c.329T>C
  • NM_001384128.1:c.329T>C
  • NM_001384130.1:c.50T>C
  • NM_001384131.1:c.329T>C
  • NM_001384132.1:c.329T>C
  • NM_001385118.1:c.329T>C
  • NM_139241.3:c.329T>C
  • NP_001291410.1:p.Leu195Pro
  • NP_001317302.1:p.Leu17Pro
  • NP_001317303.1:p.Leu17Pro
  • NP_001357227.2:p.Leu247Pro
  • NP_001371055.1:p.Leu247Pro
  • NP_001371056.1:p.Leu110Pro
  • NP_001371057.1:p.Leu110Pro
  • NP_001371059.1:p.Leu17Pro
  • NP_001371060.1:p.Leu110Pro
  • NP_001371061.1:p.Leu110Pro
  • NP_001372047.1:p.Leu110Pro
  • NP_640334.2:p.Leu110Pro
  • LRG_240t1:c.329T>C
  • LRG_240t2:c.584T>C
  • LRG_240:g.187668T>C
  • LRG_240p1:p.Leu110Pro
  • LRG_240p2:p.Leu195Pro
  • NC_000012.11:g.32735130T>C
  • NM_139241.2:c.329T>C
  • NR_168884.1:n.566T>C
Protein change:
L110P
Links:
dbSNP: rs142609007
NCBI 1000 Genomes Browser:
rs142609007
Molecular consequence:
  • NM_001304483.2:c.-516T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001304484.2:c.-823T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370297.1:c.49-16301T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001304481.1:c.584T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330373.2:c.50T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330374.2:c.50T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370298.3:c.740T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384126.1:c.740T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384127.1:c.329T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384128.1:c.329T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384130.1:c.50T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384131.1:c.329T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384132.1:c.329T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385118.1:c.329T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139241.3:c.329T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_168884.1:n.566T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000291963GeneDxcriteria provided, single submitter
Uncertain significance
(Jul 23, 2018)
germlineclinical testing

Citation Link,

SCV001143907Athena Diagnostics Inccriteria provided, single submitter
Uncertain significance
(Dec 30, 2019)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From GeneDx, SCV000291963.7

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

Description

A variant of uncertain significance has been identified in the FGD4 gene. The L110P variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The L110P variant is observed in 35/66728 (0.05%) alleles from individuals of European background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The L110P variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

From Athena Diagnostics Inc, SCV001143907.2

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

Last Updated: Oct 30, 2021

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