NM_001291303.3(FAT4):c.1599del (p.Thr534fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 24, 2022
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:: RCV002871570.3

Allele description [Variation Report for NM_001291303.3(FAT4):c.1599del (p.Thr534fs)]

NM_001291303.3(FAT4):c.1599del (p.Thr534fs)

Gene:

FAT4:FAT atypical cadherin 4 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q28.1

Genomic location:

Preferred name:

NM_001291303.3(FAT4):c.1599del (p.Thr534fs)

HGVS:

NC_000004.12:g.125318010del
NG_033865.1:g.6599del
NG_033865.2:g.8057del
NM_001291285.3:c.1599del
NM_001291303.3:c.1599delMANE SELECT
NM_024582.6:c.1599del
NP_001278214.1:p.Thr534fs
NP_001278232.1:p.Thr534fs
NP_078858.4:p.Thr534fs
NC_000004.11:g.126239164del
NC_000004.11:g.126239165del

Protein change:

T534fs

Molecular consequence:

NM_001291285.3:c.1599del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291303.3:c.1599del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024582.6:c.1599del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003232193	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 24, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24056717, 24913602, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003232193

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 24, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development.

Cappello S, Gray MJ, Badouel C, Lange S, Einsiedler M, Srour M, Chitayat D, Hamdan FF, Jenkins ZA, Morgan T, Preitner N, Uster T, Thomas J, Shannon P, Morrison V, Di Donato N, Van Maldergem L, Neuhann T, Newbury-Ecob R, Swinkells M, Terhal P, Wilson LC, et al.

Nat Genet. 2013 Nov;45(11):1300-8. doi: 10.1038/ng.2765. Epub 2013 Sep 22.

PubMed [citation]

PMID:: 24056717

Hennekam syndrome can be caused by FAT4 mutations and be allelic to Van Maldergem syndrome.

Alders M, Al-Gazali L, Cordeiro I, Dallapiccola B, Garavelli L, Tuysuz B, Salehi F, Haagmans MA, Mook OR, Majoie CB, Mannens MM, Hennekam RC.

Hum Genet. 2014 Sep;133(9):1161-7. doi: 10.1007/s00439-014-1456-y. Epub 2014 Jun 7.

PubMed [citation]

PMID:: 24913602

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003232193.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Thr534Leufs*17) in the FAT4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FAT4 are known to be pathogenic (PMID: 24056717, 24913602). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FAT4-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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