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

Germline classification:: Benign (6 submissions)
Last evaluated:: Oct 20, 2023
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:: RCV000117288.20

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

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:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000151463	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000306591	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000523316	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Feb 23, 2016)	germline	clinical testing	Citation Link,
SCV000711692	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Jan 13, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001144251	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	benign (Oct 20, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29260090, 26467025
SCV007304198	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jan 29, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	54	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

A recurrent, non-penetrant sequence variant, p.Arg266Cys in Growth/Differentiation Factor 3 (GDF3) in a female with unilateral anophthalmia and skeletal anomalies.

Bardakjian T, Krall M, Wu D, Lao R, Tang PL, Wan E, Kopinsky S, Schneider A, Kwok PY, Slavotinek A.

Am J Ophthalmol Case Rep. 2017 Sep;7:102-106. doi: 10.1016/j.ajoc.2017.06.006.

PubMed [citation]

PMID:: 29260090
PMCID:: PMC5722175

See all PubMed Citations (4)

Details of each submission

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

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

#	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

From PreventionGenetics, part of Exact Sciences, SCV000306591.1

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

#	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

From GeneDx, SCV000523316.4

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

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

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		1	not provided	1	not provided

From Athena Diagnostics, SCV001144251.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV007304198.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	54	not provided	not provided	clinical testing	PubMed (1)

#	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		54	not provided	not provided	not provided

Last Updated: Apr 12, 2026

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