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NM_001101426.4(CRPPA):c.407C>T (p.Ala136Val) AND not specified

Germline classification:
Benign (4 submissions)
Last evaluated:
Feb 23, 2016
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000117288.18

Allele description [Variation Report for NM_001101426.4(CRPPA):c.407C>T (p.Ala136Val)]

NM_001101426.4(CRPPA):c.407C>T (p.Ala136Val)

Gene:
CRPPA:CDP-L-ribitol pyrophosphorylase A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p21.2
Genomic location:
Preferred name:
NM_001101426.4(CRPPA):c.407C>T (p.Ala136Val)
HGVS:
  • NC_000007.14:g.16406188G>A
  • NG_032690.2:g.20135C>T
  • NM_001101417.4:c.407C>T
  • NM_001101426.4:c.407C>TMANE SELECT
  • NM_001368197.1:c.407C>T
  • NP_001094887.1:p.Ala136Val
  • NP_001094896.1:p.Ala136Val
  • NP_001355126.1:p.Ala136Val
  • NC_000007.13:g.16445813G>A
  • NG_032690.1:g.20135C>T
  • NM_001101426.3:c.407C>T
  • NR_160656.1:n.623C>T
Protein change:
A136V
Links:
dbSNP: rs61734789
NCBI 1000 Genomes Browser:
rs61734789
Molecular consequence:
  • NM_001101417.4:c.407C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001101426.4:c.407C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368197.1:c.407C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_160656.1:n.623C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000151463Genetic Services Laboratory, University of Chicago
no assertion criteria provided
Likely benigngermlineclinical testing

SCV000306591PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benigngermlineclinical testing

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

SCV000523316GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Feb 23, 2016)
germlineclinical testing

Citation Link,

SCV000711692Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Benign
(Jan 13, 2015)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided11not providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000151463.2

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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

From PreventionGenetics, part of Exact Sciences, SCV000306591.1

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

From GeneDx, SCV000523316.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000711692.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

p.Ala136Val in exon 2 of ISPD: This variant is not expected to have clinical sig nificance because it has been identified in 3.5% (290/8230) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs61734789).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: May 7, 2024