NM_019066.5(MAGEL2):c.1912C>T (p.Gln638Ter) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Oct 8, 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:: RCV000238706.4

Allele description [Variation Report for NM_019066.5(MAGEL2):c.1912C>T (p.Gln638Ter)]

NM_019066.5(MAGEL2):c.1912C>T (p.Gln638Ter)

Gene:

MAGEL2:MAGE family member L2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q11.2

Genomic location:

Preferred name:

NM_019066.5(MAGEL2):c.1912C>T (p.Gln638Ter)

HGVS:

NC_000015.10:g.23645831G>A
NG_016776.1:g.7016C>T
NM_019066.5:c.1912C>TMANE SELECT
NP_061939.3:p.Gln638Ter
LRG_1046t1:c.1912C>T
LRG_1046:g.7016C>T
LRG_1046p1:p.Gln638Ter
NC_000015.9:g.23890978G>A
NM_019066.4:c.1912C>T

Protein change:

Q638*; GLN638TER

Links:

OMIM: 605283.0008; dbSNP: rs797044883

NCBI 1000 Genomes Browser:

rs797044883

Molecular consequence:

NM_019066.5:c.1912C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000297290	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	criteria provided, single submitter (DGD Variant Analysis Guidelines)	Likely pathogenic (Dec 3, 2015)	unknown	clinical testing	DGD_Variant_Analysis_Guidelines.docx, Citation Link,
SCV004170148	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Oct 8, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000297290

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

criteria provided, single submitter

(DGD Variant Analysis Guidelines)

Likely pathogenic
(Dec 3, 2015)

unknown

clinical testing

DGD_Variant_Analysis_Guidelines.docx,

Citation Link,

SCV004170148

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Oct 8, 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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000297290.3

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV004170148.1

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

Description

Nonsense variant predicted to result in protein truncation, as the last 612 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27195816, 31501239, 28281571, 31791363, 29359444, 34128869, 35595280, 34051361, 37404980, 33726816, 36243518)

#	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: May 16, 2025

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