NM_001195248.2(APTX):c.513G>A (p.Leu171=) AND not provided

Clinical significance:Likely benign (Last evaluated: Apr 29, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000755827.4

Allele description [Variation Report for NM_001195248.2(APTX):c.513G>A (p.Leu171=)]

NM_001195248.2(APTX):c.513G>A (p.Leu171=)

Gene:
APTX:aprataxin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p21.1
Genomic location:
Preferred name:
NM_001195248.2(APTX):c.513G>A (p.Leu171=)
HGVS:
  • NC_000009.12:g.32986001C>T
  • NG_012821.2:g.44131G>A
  • NM_001195248.2:c.513G>AMANE SELECT
  • NM_001195249.2:c.513G>A
  • NM_001195250.2:c.351G>A
  • NM_001195251.2:c.513G>A
  • NM_001195252.2:c.297G>A
  • NM_001195254.2:c.351G>A
  • NM_001368995.1:c.513G>A
  • NM_001368996.1:c.513G>A
  • NM_001368997.1:c.513G>A
  • NM_001368998.1:c.513G>A
  • NM_001368999.1:c.513G>A
  • NM_001369000.1:c.351G>A
  • NM_001369001.1:c.351G>A
  • NM_001369002.1:c.249G>A
  • NM_001369003.1:c.249G>A
  • NM_001369004.1:c.249G>A
  • NM_001369005.1:c.249G>A
  • NM_001369006.1:c.249G>A
  • NM_001370669.1:c.249G>A
  • NM_001370670.1:c.249G>A
  • NM_001370673.1:c.249G>A
  • NM_175069.3:c.513G>A
  • NM_175073.3:c.513G>A
  • NP_001182177.2:p.Leu171=
  • NP_001182178.1:p.Leu171=
  • NP_001182179.2:p.Leu117=
  • NP_001182180.1:p.Leu171=
  • NP_001182181.2:p.Leu99=
  • NP_001182183.1:p.Leu117=
  • NP_001355924.1:p.Leu171=
  • NP_001355925.1:p.Leu171=
  • NP_001355926.1:p.Leu171=
  • NP_001355927.1:p.Leu171=
  • NP_001355928.1:p.Leu171=
  • NP_001355929.1:p.Leu117=
  • NP_001355930.1:p.Leu117=
  • NP_001355931.1:p.Leu83=
  • NP_001355932.1:p.Leu83=
  • NP_001355933.1:p.Leu83=
  • NP_001355934.1:p.Leu83=
  • NP_001355935.1:p.Leu83=
  • NP_001357598.1:p.Leu83=
  • NP_001357599.1:p.Leu83=
  • NP_001357602.1:p.Leu83=
  • NP_778239.2:p.Leu171=
  • NP_778243.1:p.Leu171=
  • NP_778243.1:p.Leu171=
  • NC_000009.11:g.32985999C>T
  • NM_175073.2:c.513G>A
  • NR_036577.2:n.464G>A
  • NR_160920.1:n.579G>A
  • NR_160921.1:n.483G>A
  • NR_160922.1:n.714G>A
  • NR_160923.1:n.518G>A
  • NR_160924.1:n.523G>A
  • NR_160925.1:n.719G>A
  • NR_160926.1:n.509G>A
  • NR_160927.1:n.829G>A
  • NR_160928.1:n.719G>A
  • NR_160929.1:n.633G>A
  • NR_160930.1:n.459G>A
  • NR_160931.1:n.698G>A
  • p.Leu171Leu
Links:
dbSNP: rs140888559
NCBI 1000 Genomes Browser:
rs140888559
Molecular consequence:
  • NR_036577.2:n.464G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160920.1:n.579G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160921.1:n.483G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160922.1:n.714G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160923.1:n.518G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160924.1:n.523G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160925.1:n.719G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160926.1:n.509G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160927.1:n.829G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160928.1:n.719G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160929.1:n.633G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160930.1:n.459G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160931.1:n.698G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001195248.2:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195249.2:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195250.2:c.351G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195251.2:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195252.2:c.297G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195254.2:c.351G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368995.1:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368996.1:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368997.1:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368998.1:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368999.1:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369000.1:c.351G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369001.1:c.351G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369002.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369003.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369004.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369005.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369006.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370669.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370670.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370673.1:c.249G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_175069.3:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_175073.3:c.513G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000883414ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratoriescriteria provided, single submitter
Likely benign
(Jun 19, 2018)
germlineclinical testing

Citation Link,

SCV001143039Athena Diagnostics Inccriteria provided, single submitter
Likely benign
(Apr 29, 2019)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000883414.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.513G>A variant (rs140888559; ClinVar Variation ID: 262911) has not been reported in the medical literature in association with disease. This variant does not alter amino acid sequence of APTX protein, affects a weakly conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant does not alter splicing. This variant is rare in the general population and is found with an overall allele frequency of 0.03% (90/271,614 alleles) in the Genome Aggregation Database. Based on available information, this variant is considered to be likely benign.

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

From Athena Diagnostics Inc, SCV001143039.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 4, 2021

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