NM_001291303.3(FAT4):c.7196T>C (p.Ile2399Thr) AND not provided

Clinical significance:Uncertain significance (Last evaluated: May 18, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001291303.3(FAT4):c.7196T>C (p.Ile2399Thr)]

NM_001291303.3(FAT4):c.7196T>C (p.Ile2399Thr)

FAT4:FAT atypical cadherin 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001291303.3(FAT4):c.7196T>C (p.Ile2399Thr)
  • NC_000004.12:g.125434422T>C
  • NG_033865.1:g.123011T>C
  • NM_001291285.3:c.7196T>C
  • NM_001291303.3:c.7196T>CMANE SELECT
  • NM_024582.4:c.7196T>C
  • NM_024582.6:c.7196T>C
  • NP_001278214.1:p.Ile2399Thr
  • NP_001278232.1:p.Ile2399Thr
  • NP_078858.4:p.Ile2399Thr
  • NP_078858.4:p.Ile2399Thr
  • NC_000004.11:g.126355577T>C
Protein change:
dbSNP: rs140285782
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001291285.3:c.7196T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001291303.3:c.7196T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024582.4:c.7196T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024582.6:c.7196T>C - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000582805GeneDxcriteria provided, single submitter
Uncertain significance
(May 18, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000582805.3

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


A variant of uncertain significance has been identified in the FAT4 gene. The I2399T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The I2399T variant is observed in 4/11558 (0.04%) alleles from individuals of Latino background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The I2399T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, this substitution occurs at a position where amino acids with similar properties to Isoleucine are tolerated across species. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Oct 25, 2021

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