NM_001291303.3(FAT4):c.9313A>G (p.Ser3105Gly) AND Van Maldergem syndrome 2

Clinical significance:Uncertain significance (Last evaluated: Dec 3, 2018)

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.9313A>G (p.Ser3105Gly)]

NM_001291303.3(FAT4):c.9313A>G (p.Ser3105Gly)

FAT4:FAT atypical cadherin 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001291303.3(FAT4):c.9313A>G (p.Ser3105Gly)
  • NC_000004.12:g.125450323A>G
  • NG_033865.1:g.138912A>G
  • NM_001291285.3:c.9313A>G
  • NM_001291303.3:c.9313A>GMANE SELECT
  • NM_024582.6:c.9307A>G
  • NP_001278214.1:p.Ser3105Gly
  • NP_001278232.1:p.Ser3105Gly
  • NP_078858.4:p.Ser3103Gly
  • NC_000004.11:g.126371478A>G
  • p.Ser3103Gly
Protein change:
dbSNP: rs764097811
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001291285.3:c.9313A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001291303.3:c.9313A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024582.6:c.9307A>G - missense variant - [Sequence Ontology: SO:0001583]


Van Maldergem syndrome 2 (VMLDS2)
MONDO: MONDO:0014242; MedGen: C3809875; Orphanet: 314679; OMIM: 615546

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001164376Broad Institute Rare Disease Group, Broad Institutecriteria provided, single submitter
Uncertain significance
(Dec 3, 2018)

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch



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 Broad Institute Rare Disease Group, Broad Institute, SCV001164376.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)


The heterozygous p.Ser3103Gly variant in FAT4 was identified by our study in the compound heterozygous state, with another VUS, in one individual with Van Maldergem syndrome. The p.Ser3103Gly variant in FAT4 has not been previously reported in individuals with Van Maldergem syndrome and has been identified in 0.003249% (1/30778) of South Asian chromosomes, 0.002980% (1/33556) of Latino chromosomes, and 0.002708% (3/110802) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs764097811). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, the clinical significance of the p.Ser3103Gly variant is uncertain. ACMG/AMP Criteria applied: PM2, BP4 (Richards 2015).

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

Last Updated: Oct 24, 2021

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