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NM_001447.3(FAT2):c.10946G>A (p.Arg3649Gln) AND Spinocerebellar ataxia 45

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Oct 15, 2018
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:
RCV000515512.1

Allele description [Variation Report for NM_001447.3(FAT2):c.10946G>A (p.Arg3649Gln)]

NM_001447.3(FAT2):c.10946G>A (p.Arg3649Gln)

Genes:
FAT2:FAT atypical cadherin 2 [Gene - OMIM - HGNC]
SLC36A1:solute carrier family 36 member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q33.1
Genomic location:
Preferred name:
NM_001447.3(FAT2):c.10946G>A (p.Arg3649Gln)
HGVS:
  • NC_000005.10:g.151521647C>T
  • NG_046979.1:g.135494G>A
  • NM_001447.3:c.10946G>AMANE SELECT
  • NP_001438.1:p.Arg3649Gln
  • NP_001438.1:p.Arg3649Gln
  • NC_000005.9:g.150901208C>T
  • NM_001447.2:c.10946G>A
Protein change:
R3649Q; ARG3649GLN
Links:
OMIM: 604269.0002; dbSNP: rs201335279
NCBI 1000 Genomes Browser:
rs201335279
Molecular consequence:
  • NM_001447.3:c.10946G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Spinocerebellar ataxia 45
Identifiers:
MONDO: MONDO:0033480; MedGen: C4540400; OMIM: 617769

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000611608OMIM
no assertion criteria provided
Pathogenic
(Nov 16, 2017)
germlineliterature only

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

SCV000883164SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Oct 15, 2018)
germlinecuration

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Exome sequencing and network analysis identifies shared mechanisms underlying spinocerebellar ataxia.

Nibbeling EAR, Duarri A, Verschuuren-Bemelmans CC, Fokkens MR, Karjalainen JM, Smeets CJLM, de Boer-Bergsma JJ, van der Vries G, Dooijes D, Bampi GB, van Diemen C, Brunt E, Ippel E, Kremer B, Vlak M, Adir N, Wijmenga C, van de Warrenburg BPC, Franke L, Sinke RJ, Verbeek DS.

Brain. 2017 Nov 1;140(11):2860-2878. doi: 10.1093/brain/awx251.

PubMed [citation]
PMID:
29053796

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 OMIM, SCV000611608.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a man (case DNA056251) with spinocerebellar ataxia-45 (SCA45; 617769), Nibbeling et al. (2017) identified a heterozygous c.10946G-A transition (chr5.150901208, GRCh37) in the FAT2 gene, resulting in an arg3649-to-gln (R3649Q) substitution at a highly conserved residue in the linker between the last cadherin repeat and the laminin A-G motif. The mutation was found by exome sequencing using a gene panel and confirmed by Sanger sequencing.

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

From SIB Swiss Institute of Bioinformatics, SCV000883164.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)

Description

This variant is interpreted as Uncertain Significance - Insufficient Evidence, for Spinocerebellar ataxia 45, autosomal dominant. The following ACMG Tag(s) were applied: PM2-Supporting => PM2 downgraded in strength to Supporting. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product (https://www.ncbi.nlm.nih.gov/pubmed/29053796).

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

Last Updated: Apr 23, 2022