NM_033409.4(SLC52A3):c.775C>T (p.Gln259Ter) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 21, 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:: RCV002409704.2

Allele description [Variation Report for NM_033409.4(SLC52A3):c.775C>T (p.Gln259Ter)]

NM_033409.4(SLC52A3):c.775C>T (p.Gln259Ter)

Gene:

SLC52A3:solute carrier family 52 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_033409.4(SLC52A3):c.775C>T (p.Gln259Ter)

HGVS:

NC_000020.11:g.763796G>A
NG_027687.2:g.17190C>T
NM_001370085.1:c.775C>T
NM_001370086.1:c.775C>T
NM_033409.4:c.775C>TMANE SELECT
NP_001357014.1:p.Gln259Ter
NP_001357015.1:p.Gln259Ter
NP_212134.3:p.Gln259Ter
LRG_1394t1:c.775C>T
LRG_1394:g.17190C>T
LRG_1394p1:p.Gln259Ter
NC_000020.10:g.744440G>A
NM_033409.3:c.775C>T

Protein change:

Q259*

Molecular consequence:

NM_001370085.1:c.775C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370086.1:c.775C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_033409.4:c.775C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002672186	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Mar 21, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002672186

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Mar 21, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV002672186.2

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

Description

The p.Q259* pathogenic mutation (also known as c.775C>T), located in coding exon 2 of the SLC52A3 gene, results from a C to T substitution at nucleotide position 775. This changes the amino acid from a glutamine to a stop codon within coding exon 2. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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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