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NM_001291303.3(FAT4):c.10483A>G (p.Ser3495Gly) AND Hennekam lymphangiectasia-lymphedema syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 29, 2024
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:
RCV004560089.1

Allele description [Variation Report for NM_001291303.3(FAT4):c.10483A>G (p.Ser3495Gly)]

NM_001291303.3(FAT4):c.10483A>G (p.Ser3495Gly)

Gene:
FAT4:FAT atypical cadherin 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q28.1
Genomic location:
Preferred name:
NM_001291303.3(FAT4):c.10483A>G (p.Ser3495Gly)
HGVS:
  • NC_000004.12:g.125451493A>G
  • NG_033865.2:g.141540A>G
  • NM_001291285.3:c.10483A>G
  • NM_001291303.3:c.10483A>GMANE SELECT
  • NM_024582.6:c.10477A>G
  • NP_001278214.1:p.Ser3495Gly
  • NP_001278232.1:p.Ser3495Gly
  • NP_078858.4:p.Ser3493Gly
  • NC_000004.11:g.126372648A>G
  • NG_033865.1:g.140082A>G
Protein change:
S3493G
Molecular consequence:
  • NM_001291285.3:c.10483A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001291303.3:c.10483A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024582.6:c.10477A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hennekam lymphangiectasia-lymphedema syndrome 2 (HKLLS2)
Identifiers:
MONDO: MONDO:0014454; MedGen: C4014939; Orphanet: 2136; OMIM: 616006

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV005047076Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Mar 29, 2024)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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 Clinical Genomics Laboratory, Washington University in St. Louis, SCV005047076.1

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

Description

The FAT4 c.10483A>G (p.Ser3495Gly) variant was identified at a near heterozygous allele fraction of 49%, a frequency which may be consistent with it being of germline origin. This variant, to our knowledge, has not been reported in the medical literature. Computational predictors suggest that this variant does not impact FAT4 function. The FAT4 c.10483A>G (p.Ser3495Gly) variant has been reported in the ClinVar database as a variant of uncertain significance by one submitter (ClinVar ID: 2419888). This variant is only observed on 10/1,614,002 alleles in the general population (gnomAD v4.0.0), indicating it is not a common variant. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of the FAT4 c.10483A>G (p.Ser3495Gly) variant is uncertain at this time.

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

Last Updated: Sep 29, 2024