NM_000169.3(GLA):c.124A>C (p.Met42Leu) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Nov 13, 2024
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:: RCV000235742.10

Allele description [Variation Report for NM_000169.3(GLA):c.124A>C (p.Met42Leu)]

NM_000169.3(GLA):c.124A>C (p.Met42Leu)

Genes:

RPL36A-HNRNPH2:RPL36A-HNRNPH2 readthrough [Gene - HGNC]
GLA:galactosidase alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq22.1

Genomic location:

Preferred name:

NM_000169.3(GLA):c.124A>C (p.Met42Leu)

HGVS:

NC_000023.11:g.101407780T>G
NG_007119.1:g.5184A>C
NG_016327.1:g.4578T>G
NM_000169.3:c.124A>CMANE SELECT
NM_001199973.2:c.301-4156T>G
NM_001199974.2:c.178-4156T>G
NM_001406747.1:c.124A>C
NM_001406748.1:c.124A>C
NM_001406749.1:c.124A>C
NP_000160.1:p.Met42Leu
NP_000160.1:p.Met42Leu
NP_001393676.1:p.Met42Leu
NP_001393677.1:p.Met42Leu
NP_001393678.1:p.Met42Leu
LRG_672t1:c.124A>C
LRG_672:g.5184A>C
LRG_672p1:p.Met42Leu
NC_000023.10:g.100662768T>G
NM_000169.2:c.124A>C
NR_164783.1:n.146A>C
NR_176252.1:n.146A>C
NR_176253.1:n.146A>C
P06280:p.Met42Leu

Protein change:

M42L

Links:

UniProtKB: P06280#VAR_062551; dbSNP: rs797044613

NCBI 1000 Genomes Browser:

rs797044613

Molecular consequence:

NM_001199973.2:c.301-4156T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001199974.2:c.178-4156T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000169.3:c.124A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406747.1:c.124A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406748.1:c.124A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406749.1:c.124A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_164783.1:n.146A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176252.1:n.146A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176253.1:n.146A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000293385	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Nov 13, 2024)	germline	clinical testing	Citation Link,
SCV000331633	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Jun 26, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000293385

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Nov 13, 2024)

germline

clinical testing

Citation Link,

SCV000331633

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Pathogenic
(Jun 26, 2017)

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	10	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000293385.11

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

Description

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: 10666480, 17391432, 25382311, 35653365, 30386727, 15712228, 27657681, 31036492, 15492942)

#	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 Eurofins Ntd Llc (ga), SCV000331633.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	10	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		10	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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