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NM_001370298.3(FGD4):c.643G>A (p.Asp215Asn) AND Charcot-Marie-Tooth disease type 4

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 19, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002634253.2

Allele description

NM_001370298.3(FGD4):c.643G>A (p.Asp215Asn)

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.643G>A (p.Asp215Asn)
HGVS:
  • NC_000012.12:g.32582099G>A
  • NG_008626.2:g.187571G>A
  • NM_001304481.2:c.487G>A
  • NM_001304483.2:c.-613G>A
  • NM_001304484.2:c.-920G>A
  • NM_001330373.2:c.-48G>A
  • NM_001330374.2:c.-48G>A
  • NM_001370297.1:c.49-16398G>A
  • NM_001370298.3:c.643G>AMANE SELECT
  • NM_001384126.1:c.643G>A
  • NM_001384127.1:c.232G>A
  • NM_001384128.1:c.232G>A
  • NM_001384130.1:c.-48G>A
  • NM_001384131.1:c.232G>A
  • NM_001384132.1:c.232G>A
  • NM_001385118.1:c.232G>A
  • NM_139241.3:c.232G>A
  • NP_001291410.1:p.Asp163Asn
  • NP_001291410.1:p.Asp163Asn
  • NP_001357227.2:p.Asp215Asn
  • NP_001371055.1:p.Asp215Asn
  • NP_001371056.1:p.Asp78Asn
  • NP_001371057.1:p.Asp78Asn
  • NP_001371060.1:p.Asp78Asn
  • NP_001371061.1:p.Asp78Asn
  • NP_001372047.1:p.Asp78Asn
  • NP_640334.2:p.Asp78Asn
  • LRG_240t1:c.232G>A
  • LRG_240t2:c.487G>A
  • LRG_240:g.187571G>A
  • LRG_240p1:p.Asp78Asn
  • LRG_240p2:p.Asp163Asn
  • NC_000012.11:g.32735033G>A
  • NM_001304481.1:c.487G>A
  • NR_168884.1:n.469G>A
Protein change:
D163N
Molecular consequence:
  • NM_001304483.2:c.-613G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001304484.2:c.-920G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001330373.2:c.-48G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001330374.2:c.-48G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001384130.1:c.-48G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001370297.1:c.49-16398G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001304481.2:c.487G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370298.3:c.643G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384126.1:c.643G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384127.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384128.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384131.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384132.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385118.1:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_139241.3:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_168884.1:n.469G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Charcot-Marie-Tooth disease type 4
Synonyms:
Charcot-Marie-Tooth, Type 4
Identifiers:
MONDO: MONDO:0018995; MedGen: C4082197

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003520168Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 19, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV003520168.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with FGD4-related conditions. This variant is present in population databases (rs760087704, gnomAD 0.0009%). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 78 of the FGD4 protein (p.Asp78Asn).

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

Last Updated: Feb 14, 2024