NM_006164.5(NFE2L2):c.204A>C (p.Lys68Asn) AND Immunodeficiency, developmental delay, and hypohomocysteinemia

Germline classification:: Uncertain significance (1 submission)
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:: RCV003338079.2

Allele description [Variation Report for NM_006164.5(NFE2L2):c.204A>C (p.Lys68Asn)]

NM_006164.5(NFE2L2):c.204A>C (p.Lys68Asn)

Gene:

NFE2L2:NFE2 like bZIP transcription factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.2

Genomic location:

Preferred name:

NM_006164.5(NFE2L2):c.204A>C (p.Lys68Asn)

HGVS:

NC_000002.12:g.177234113T>G
NM_001145412.3:c.156A>C
NM_001145413.3:c.156A>C
NM_001313900.1:c.156A>C
NM_001313901.1:c.156A>C
NM_001313902.2:c.204A>C
NM_001313903.2:c.93+111A>C
NM_001313904.1:c.-26A>C
NM_006164.5:c.204A>CMANE SELECT
NP_001138884.1:p.Lys52Asn
NP_001138885.1:p.Lys52Asn
NP_001300829.1:p.Lys52Asn
NP_001300830.1:p.Lys52Asn
NP_001300831.1:p.Lys68Asn
NP_006155.2:p.Lys68Asn
NC_000002.11:g.178098841T>G

Protein change:

K52N

Molecular consequence:

NM_001313904.1:c.-26A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001313903.2:c.93+111A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001145412.3:c.156A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145413.3:c.156A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001313900.1:c.156A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001313901.1:c.156A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001313902.2:c.204A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006164.5:c.204A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Immunodeficiency, developmental delay, and hypohomocysteinemia
Identifiers:: MONDO: MONDO:0060591; MedGen: C4540293; OMIM: 617744

Recent activity

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SAMN44502830 (1)
SRA
PREDICTED: Mus musculus popeye domain containing 2 (Popdc2), transcript variant ...
PREDICTED: Mus musculus popeye domain containing 2 (Popdc2), transcript variant X2, mRNA
gi|1720387549|ref|XM_006522439.4|

Nucleotide
urinary protein 2-like [Rattus norvegicus]
urinary protein 2-like [Rattus norvegicus]
gi|1958798513|ref|XP_038938228.1|

Protein
Lepus californicus texianus strain ECOSCM 9504 cytochrome b (cytb) gene, partial...
Lepus californicus texianus strain ECOSCM 9504 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|2294292206|gb|MW940636.1|

Nucleotide
prostaglandin E2 receptor EP2 subtype [Mus musculus]
prostaglandin E2 receptor EP2 subtype [Mus musculus]
gi|6679529|ref|NP_032990.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004046977	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004046977

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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	yes	not provided	not provided	not provided	not provided	not provided	clinical 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

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004046977.1

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

Description

The c.204A>C (p.Lys68Asn) missense variant in NFE2L2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Lys68Asn variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The amino acid Lys at position 68 is changed to a Asn changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by SIFT and the residue is variable across species. The amino acid change p.Lys68Asn in NFE2L2 is predicted as conserved by PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

#	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: Apr 6, 2024

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