NM_001370298.3(FGD4):c.1808_1809del (p.Thr603fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 14, 2018
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:: RCV000255773.2

Allele description [Variation Report for NM_001370298.3(FGD4):c.1808_1809del (p.Thr603fs)]

NM_001370298.3(FGD4):c.1808_1809del (p.Thr603fs)

Gene:

FGD4:FYVE, RhoGEF and PH domain containing 4 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

12p11.21

Genomic location:

Preferred name:

NM_001370298.3(FGD4):c.1808_1809del (p.Thr603fs)

HGVS:

NC_000012.12:g.32619754CA[1]
NG_008626.2:g.225226CA[1]
NM_001304481.2:c.1650_1651CA[1]
NM_001304483.2:c.653_654del
NM_001304484.2:c.365_366del
NM_001330373.2:c.1118_1119del
NM_001330374.2:c.1118_1119del
NM_001370297.1:c.845_846del
NM_001370298.3:c.1808_1809delMANE SELECT
NM_001384126.1:c.1808_1809del
NM_001384127.1:c.1397_1398del
NM_001384128.1:c.1397_1398del
NM_001384130.1:c.1118_1119del
NM_001385118.1:c.1397_1398del
NM_139241.3:c.1397_1398del
NP_001291410.1:p.Thr551Serfs
NP_001291410.1:p.Thr551fs
NP_001291412.1:p.Thr218fs
NP_001291413.1:p.Thr122fs
NP_001317302.1:p.Thr373fs
NP_001317303.1:p.Thr373fs
NP_001357226.1:p.Thr282fs
NP_001357227.2:p.Thr603fs
NP_001371055.1:p.Thr603fs
NP_001371056.1:p.Thr466fs
NP_001371057.1:p.Thr466fs
NP_001371059.1:p.Thr373fs
NP_001372047.1:p.Thr466fs
NP_640334.2:p.Thr466fs
LRG_240t1:c.1397_1398del
LRG_240t2:c.1652_1653del
LRG_240:g.225226CA[1]
LRG_240p1:p.Thr466fs
LRG_240p2:p.Thr551fs
NC_000012.11:g.32772688CA[1]
NM_001304481.1:c.1652_1653del
NM_139241.2:c.1397_1398delCA

Protein change:

T122fs

Links:

dbSNP: rs886039361

NCBI 1000 Genomes Browser:

rs886039361

Molecular consequence:

NM_001304481.2:c.1650_1651CA[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304483.2:c.653_654del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304484.2:c.365_366del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330373.2:c.1118_1119del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330374.2:c.1118_1119del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370297.1:c.845_846del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370298.3:c.1808_1809del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001384126.1:c.1808_1809del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001384127.1:c.1397_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001384128.1:c.1397_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001384130.1:c.1118_1119del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001385118.1:c.1397_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_139241.3:c.1397_1398del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000321635	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Sep 14, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000321635

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Sep 14, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000321635.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.1397_1398delCA variant in the FGD4 gene causes a frameshift starting with codon Threonine 466, changes this amino acid to a Serine residue and creates a premature Stop codon at position 8 of the new reading frame, denoted p.Thr466SerfsX8. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Although this variant has not been previously reported to our knowledge, it is interpreted to be a pathogenic variant.

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

Last Updated: Jan 7, 2023

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