NM_080632.3(UPF3B):c.674_677del (p.Arg225fs) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Feb 2, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000494240.30

Allele description [Variation Report for NM_080632.3(UPF3B):c.674_677del (p.Arg225fs)]

NM_080632.3(UPF3B):c.674_677del (p.Arg225fs)

Gene:

UPF3B:UPF3B regulator of nonsense mediated mRNA decay [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

Xq24

Genomic location:

Preferred name:

NM_080632.3(UPF3B):c.674_677del (p.Arg225fs)

HGVS:

NC_000023.11:g.119841207TTCT[1]
NG_009241.1:g.16793GAAA[1]
NM_023010.4:c.674_677del
NM_080632.2:c.674_677delGAAA
NM_080632.3:c.674_677delMANE SELECT
NP_075386.1:p.Arg225fs
NP_542199.1:p.Arg225fs
NC_000023.10:g.118975169_118975172del
NC_000023.10:g.118975170TTCT[1]
NM_080632.1:c.674_677del
NM_080632.1:c.674_677delGAAA
NM_080632.2:c.674_677del
p.Arg225Lysfs*22

Protein change:

R225fs

Links:

OMIM: 300298.0001; dbSNP: rs794727881

NCBI 1000 Genomes Browser:

rs794727881

Molecular consequence:

NM_023010.4:c.674_677del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080632.3:c.674_677del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

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
SCV000232325	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Dec 2, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000583293	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Feb 2, 2022)	germline	clinical testing	Citation Link,
SCV001247900	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Feb 1, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000232325

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Dec 2, 2014)

germline

clinical testing

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

Citation Link,

SCV000583293

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Feb 2, 2022)

germline

clinical testing

Citation Link,

SCV001247900

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Feb 1, 2019)

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	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	5	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

Tarpey PS, Raymond FL, Nguyen LS, Rodriguez J, Hackett A, Vandeleur L, Smith R, Shoubridge C, Edkins S, Stevens C, O'Meara S, Tofts C, Barthorpe S, Buck G, Cole J, Halliday K, Hills K, Jones D, Mironenko T, Perry J, Varian J, West S, et al.

Nat Genet. 2007 Sep;39(9):1127-33. Epub 2007 Aug 19.

PubMed [citation]

PMID:: 17704778
PMCID:: PMC2872770

Details of each submission

From Eurofins Ntd Llc (ga), SCV000232325.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	PubMed (1)

#	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		5	not provided	not provided	not provided

From GeneDx, SCV000583293.6

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 17704778, 26012578, 19377476, 24665081)

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001247900.26

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

#	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		2	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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