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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:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

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

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

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:
Genomic location:
Preferred name:
NM_001447.3(FAT2):c.10946G>A (p.Arg3649Gln)
  • 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
OMIM: 604269.0002; dbSNP: rs201335279
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001447.3:c.10946G>A - missense variant - [Sequence Ontology: SO:0001583]


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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
no assertion criteria provided
(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)

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



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]

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]

Details of each submission

From OMIM, SCV000611608.1

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


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.

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)


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).

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

Last Updated: Apr 23, 2022