NM_014053.4(FLVCR1):c.1547G>A (p.Arg516Gln) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Aug 11, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001379271.1

Allele description [Variation Report for NM_014053.4(FLVCR1):c.1547G>A (p.Arg516Gln)]

NM_014053.4(FLVCR1):c.1547G>A (p.Arg516Gln)

Gene:
FLVCR1:FLVCR heme transporter 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q32.3
Genomic location:
Preferred name:
NM_014053.4(FLVCR1):c.1547G>A (p.Arg516Gln)
HGVS:
  • NC_000001.11:g.212895007G>A
  • NG_028131.1:g.41753G>A
  • NM_014053.4:c.1547G>AMANE SELECT
  • NP_054772.1:p.Arg516Gln
  • NC_000001.10:g.213068349G>A
Protein change:
R516Q
Molecular consequence:
  • NM_014053.4:c.1547G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001577042Invitaecriteria provided, single submitter
Likely pathogenic
(Aug 11, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Autosomal recessive posterior column ataxia with retinitis pigmentosa caused by novel mutations in the FLVCR1 gene.

Shaibani A, Wong LJ, Wei Zhang V, Lewis RA, Shinawi M.

Int J Neurosci. 2015 Jan;125(1):43-9. doi: 10.3109/00207454.2014.904858. Epub 2014 May 16.

PubMed [citation]
PMID:
24628582

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001577042.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces arginine with glutamine at codon 516 of the FLVCR1 protein (p.Arg516Gln). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs780752648, ExAC 0.02%). This variant has been observed in individual(s) with posterior column ataxia with retinitis pigmentosa (PMID: 24628582). It has also been observed to segregate with disease in related individuals. 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: Tolerated; PolyPhen-2: Possibly Damaging; Align-GVGD: Class C0). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: May 14, 2021

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