NM_000110.4(DPYD):c.775A>G (p.Lys259Glu) AND Inborn genetic diseases

Germline classification:: Likely benign (1 submission)
Last evaluated:: Mar 16, 2018
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:: RCV002408943.2

Allele description [Variation Report for NM_000110.4(DPYD):c.775A>G (p.Lys259Glu)]

NM_000110.4(DPYD):c.775A>G (p.Lys259Glu)

Gene:

DPYD:dihydropyrimidine dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p21.3

Genomic location:

Preferred name:

NM_000110.4(DPYD):c.775A>G (p.Lys259Glu)

HGVS:

NC_000001.11:g.97679170T>C
NG_008807.2:g.246890A>G
NM_000110.4:c.775A>GMANE SELECT
NP_000101.2:p.Lys259Glu
NP_000101.2:p.Lys259Glu
LRG_722t1:c.775A>G
LRG_722:g.246890A>G
LRG_722p1:p.Lys259Glu
NC_000001.10:g.98144726T>C
NM_000110.3:c.775A>G

Protein change:

K259E

Links:

dbSNP: rs45589337

NCBI 1000 Genomes Browser:

rs45589337

Molecular consequence:

NM_000110.4:c.775A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002672183	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Mar 16, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 14635116, 19473056, 24648345 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002672183

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Mar 16, 2018)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

Detailed analysis of five mutations in dihydropyrimidine dehydrogenase detected in cancer patients with 5-fluorouracil-related side effects.

Gross E, Ullrich T, Seck K, Mueller V, de Wit M, von Schilling C, Meindl A, Schmitt M, Kiechle M.

Hum Mutat. 2003 Dec;22(6):498.

PubMed [citation]

PMID:: 14635116

Influence of dihydropyrimidine dehydrogenase gene (DPYD) coding sequence variants on the development of fluoropyrimidine-related toxicity in patients with high-grade toxicity and patients with excellent tolerance of fluoropyrimidine-based chemotherapy.

Kleibl Z, Fidlerova J, Kleiblova P, Kormunda S, Bilek M, Bouskova K, Sevcik J, Novotny J.

Neoplasma. 2009;56(4):303-16.

PubMed [citation]

PMID:: 19473056

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV002672183.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: Apr 20, 2025

ClinVar

Relating variation to medicine