U.S. flag

An official website of the United States government

NM_000485.3(APRT):c.388_397del (p.Leu130fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 5, 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:
RCV003670920.2

Allele description [Variation Report for NM_000485.3(APRT):c.388_397del (p.Leu130fs)]

NM_000485.3(APRT):c.388_397del (p.Leu130fs)

Gene:
APRT:adenine phosphoribosyltransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000485.3(APRT):c.388_397del (p.Leu130fs)
HGVS:
  • NC_000016.10:g.88810076_88810085del
  • NG_008013.1:g.6853_6862del
  • NG_028266.1:g.11299_11308del
  • NM_000485.3:c.388_397delMANE SELECT
  • NM_001030018.2:c.388_397del
  • NP_000476.1:p.Leu130fs
  • NP_001025189.1:p.Leu130fs
  • NC_000016.9:g.88876481_88876490del
  • NC_000016.9:g.88876484_88876493del
Protein change:
L130fs
Molecular consequence:
  • NM_000485.3:c.388_397del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001030018.2:c.388_397del - frameshift variant - [Sequence Ontology: SO:0001589]

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

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004393564Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 5, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004393564.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the APRT protein in which other variant(s) (p.Leu162del) have been determined to be pathogenic (Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with APRT-related conditions. This variant is present in population databases (rs775204282, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Leu130Valfs*4) in the APRT gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 51 amino acid(s) of the APRT protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024