NM_002906.4(RDX):c.682_685del (p.Tyr228fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 6, 2017
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:: RCV001382842.4

Allele description [Variation Report for NM_002906.4(RDX):c.682_685del (p.Tyr228fs)]

NM_002906.4(RDX):c.682_685del (p.Tyr228fs)

Gene:

RDX:radixin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_002906.4(RDX):c.682_685del (p.Tyr228fs)

HGVS:

NC_000011.10:g.110257780_110257783del
NG_023044.2:g.43930_43933del
NM_001260492.2:c.682_685del
NM_001260493.2:c.682_685del
NM_001260494.2:c.274_277del
NM_001260495.2:c.-82-9950_-82-9947del
NM_001260496.2:c.404+374_404+377del
NM_002906.4:c.682_685delMANE SELECT
NP_001247421.1:p.Tyr228fs
NP_001247422.1:p.Tyr228fs
NP_001247423.1:p.Tyr92fs
NP_002897.1:p.Tyr228fs
NC_000011.9:g.110128505_110128508del
NC_000011.9:g.110128505_110128508delCATA

Protein change:

Y228fs

Links:

dbSNP: rs2134363728

NCBI 1000 Genomes Browser:

rs2134363728

Molecular consequence:

NM_001260492.2:c.682_685del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001260493.2:c.682_685del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001260494.2:c.274_277del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002906.4:c.682_685del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001260495.2:c.-82-9950_-82-9947del - intron variant - [Sequence Ontology: SO:0001627]
NM_001260496.2:c.404+374_404+377del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV001581788	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 6, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12068294, 17226784, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001581788

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 6, 2017)

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

Radixin deficiency causes conjugated hyperbilirubinemia with loss of Mrp2 from bile canalicular membranes.

Kikuchi S, Hata M, Fukumoto K, Yamane Y, Matsui T, Tamura A, Yonemura S, Yamagishi H, Keppler D, Tsukita S, Tsukita S.

Nat Genet. 2002 Jul;31(3):320-5. Epub 2002 Jun 17.

PubMed [citation]

PMID:: 12068294

Mutations of the RDX gene cause nonsyndromic hearing loss at the DFNB24 locus.

Khan SY, Ahmed ZM, Shabbir MI, Kitajiri S, Kalsoom S, Tasneem S, Shayiq S, Ramesh A, Srisailpathy S, Khan SN, Smith RJ, Riazuddin S, Friedman TB, Riazuddin S.

Hum Mutat. 2007 May;28(5):417-23.

PubMed [citation]

PMID:: 17226784

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001581788.4

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

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in RDX are known to be pathogenic (PMID: 12068294, 17226784). This variant has not been reported in the literature in individuals with RDX-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Tyr228Serfs*6) in the RDX gene. It is expected to result in an absent or disrupted protein product.

#	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: Feb 14, 2024

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