NM_001077350.3(NPRL3):c.1270C>T (p.Arg424Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 8, 2023
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:: RCV002281079.3

Allele description [Variation Report for NM_001077350.3(NPRL3):c.1270C>T (p.Arg424Ter)]

NM_001077350.3(NPRL3):c.1270C>T (p.Arg424Ter)

Genes:

NPRL3:NPR3 like, GATOR1 complex subunit [Gene - OMIM - HGNC]
HBA-LCR:alpha-globin locus control region [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_001077350.3(NPRL3):c.1270C>T (p.Arg424Ter)

HGVS:

NC_000016.10:g.89794G>A
NG_029669.1:g.53906C>T
NG_042799.1:g.2087G>A
NM_001039476.3:c.733C>T
NM_001077350.3:c.1270C>TMANE SELECT
NM_001243247.2:c.1036C>T
NM_001243248.2:c.1195C>T
NM_001243249.2:c.1195C>T
NP_001034565.1:p.Arg245Ter
NP_001070818.1:p.Arg424Ter
NP_001230176.1:p.Arg346Ter
NP_001230177.1:p.Arg399Ter
NP_001230178.1:p.Arg399Ter
NC_000016.9:g.139792G>A
NM_001077350.1:c.1270C>T
NM_001077350.2:c.1270C>T

Protein change:

R245*; ARG424TER

Links:

OMIM: 600928.0004; dbSNP: rs886037961

NCBI 1000 Genomes Browser:

rs886037961

Molecular consequence:

NM_001039476.3:c.733C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001077350.3:c.1270C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001243247.2:c.1036C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001243248.2:c.1195C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001243249.2:c.1195C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002569770	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 8, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002569770

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(May 8, 2023)

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, SCV002569770.3

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

Description

Reported previously in an individual with refractory focal epilepsy (Abumurad et al., 221); Nonsense 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: 34868250, 34693554, 33461085, 33741238, 30093711, 27173016, 30485578, 36864519, 37099548, 34235417, 36937533)

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine