NM_001128159.3(VPS53):c.1499T>C (p.Ile500Thr) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 26, 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:: RCV002678223.2

Allele description [Variation Report for NM_001128159.3(VPS53):c.1499T>C (p.Ile500Thr)]

NM_001128159.3(VPS53):c.1499T>C (p.Ile500Thr)

Gene:

VPS53:VPS53 subunit of GARP complex [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.3

Genomic location:

Preferred name:

NM_001128159.3(VPS53):c.1499T>C (p.Ile500Thr)

HGVS:

NC_000017.11:g.562560A>G
NG_034190.1:g.157297T>C
NM_001128159.3:c.1499T>CMANE SELECT
NM_001366253.2:c.1499T>C
NM_001366254.2:c.905T>C
NM_018289.4:c.1412T>C
NP_001121631.1:p.Ile500Thr
NP_001353182.1:p.Ile500Thr
NP_001353183.1:p.Ile302Thr
NP_060759.2:p.Ile471Thr
NC_000017.10:g.465800A>G
NM_001128159.2:c.1499T>C

Protein change:

I302T

Molecular consequence:

NM_001128159.3:c.1499T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001366253.2:c.1499T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001366254.2:c.905T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_018289.4:c.1412T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 5,...
Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 5, mRNA
gi|1675172632|ref|NM_181305.3|

Nucleotide
Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 6,...
Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 6, mRNA
gi|1676318617|ref|NM_181306.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003549594	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Oct 26, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003549594

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Oct 26, 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, SCV003549594.2

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

Description

The c.1499T>C (p.I500T) alteration is located in exon 14 (coding exon 14) of the VPS53 gene. This alteration results from a T to C substitution at nucleotide position 1499, causing the isoleucine (I) at amino acid position 500 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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