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NM_001291303.3(FAT4):c.6094A>G (p.Thr2032Ala) AND Hennekam lymphangiectasia-lymphedema syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 29, 2023
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:
RCV003458201.1

Allele description [Variation Report for NM_001291303.3(FAT4):c.6094A>G (p.Thr2032Ala)]

NM_001291303.3(FAT4):c.6094A>G (p.Thr2032Ala)

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.6094A>G (p.Thr2032Ala)
HGVS:
  • NC_000004.12:g.125415057A>G
  • NG_033865.1:g.103646A>G
  • NM_001291285.3:c.6094A>G
  • NM_001291303.3:c.6094A>GMANE SELECT
  • NM_024582.6:c.6094A>G
  • NP_001278214.1:p.Thr2032Ala
  • NP_001278232.1:p.Thr2032Ala
  • NP_078858.4:p.Thr2032Ala
  • NP_078858.4:p.Thr2032Ala
  • NC_000004.11:g.126336212A>G
  • NM_024582.4:c.6094A>G
Protein change:
T2032A
Links:
dbSNP: rs147314754
NCBI 1000 Genomes Browser:
rs147314754
Molecular consequence:
  • NM_001291285.3:c.6094A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001291303.3:c.6094A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024582.6:c.6094A>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
SCV004177063Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Sep 29, 2023)
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, SCV004177063.1

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

Description

The FAT4 c.6094A>G (p.Thr2032Ala) variant was identified at a near heterozygous allelic fraction. This variant, to our knowledge, has not been reported in the literature. This variant has been reported in the ClinVar database as a variant of uncertain significance by multiple submitters and likely benign variant by one submitter (ClinVar ID: 426899). Computational predictors are uncertain as to the impact of this variant on FAT4 function. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

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

Last Updated: Sep 29, 2024