NM_000402.4(G6PD):c.1406G>C (p.Arg469Pro) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Nov 14, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000723442.12

Allele description [Variation Report for NM_000402.4(G6PD):c.1406G>C (p.Arg469Pro)]

NM_000402.4(G6PD):c.1406G>C (p.Arg469Pro)

Gene:

G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_000402.4(G6PD):c.1406G>C (p.Arg469Pro)

Other names:

G6PD, ARG439PRO; G6PD Pawnee

HGVS:

NC_000023.11:g.154532434C>G
NG_009015.2:g.20139G>C
NM_000402.4:c.1406G>C
NM_001042351.3:c.1316G>C
NM_001360016.2:c.1316G>CMANE SELECT
NP_000393.4:p.Arg469Pro
NP_001035810.1:p.Arg439Pro
NP_001346945.1:p.Arg439Pro
NC_000023.10:g.153760649C>G
NM_001042351.1:c.1316G>C
NM_001042351.3:c.1316G>C

Protein change:

R439P; ARG439PRO

Links:

OMIM: 305900.0040; dbSNP: rs137852337

NCBI 1000 Genomes Browser:

rs137852337

Molecular consequence:

NM_000402.4:c.1406G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001042351.3:c.1316G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001360016.2:c.1316G>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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unnamed protein product [Mus musculus]
unnamed protein product [Mus musculus]
gi|12836542|dbj|BAB23701.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000700390	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Jan 6, 2017)	germline	clinical testing	Citation Link,
SCV000883926	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely pathogenic (Jul 23, 2017)	germline	clinical testing	Citation Link,
SCV005201600	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Nov 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000700390

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Jan 6, 2017)

germline

clinical testing

Citation Link,

SCV000883926

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely pathogenic
(Jul 23, 2017)

germline

clinical testing

Citation Link,

SCV005201600

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Nov 14, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000700390.2

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

#	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		2	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000883926.1

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

#	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, SCV005201600.1

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

Description

Identified in individuals with features of G6PD deficiency and described as the Pawnee variant (PMID: 1611091); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30206300, 2190319, 22293322, 1611091)

#	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

Last Updated: Oct 20, 2024

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