NM_133642.5(LARGE1):c.1788G>A (p.Ala596=) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Dec 1, 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:: RCV000710158.23

Allele description [Variation Report for NM_133642.5(LARGE1):c.1788G>A (p.Ala596=)]

NM_133642.5(LARGE1):c.1788G>A (p.Ala596=)

Gene:

LARGE1:LARGE xylosyl- and glucuronyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.3

Genomic location:

Preferred name:

NM_133642.5(LARGE1):c.1788G>A (p.Ala596=)

HGVS:

NC_000022.11:g.33283291C>T
NG_009929.2:g.642138G>A
NM_001362949.2:c.1788G>A
NM_001362951.2:c.1788G>A
NM_001362953.2:c.1788G>A
NM_001378624.1:c.1788G>A
NM_001378625.1:c.1788G>A
NM_001378626.1:c.1788G>A
NM_001378627.1:c.1731-6036G>A
NM_001378628.1:c.1731-6036G>A
NM_001378629.1:c.1632G>A
NM_001378630.1:c.1185G>A
NM_001378631.1:c.972-6036G>A
NM_004737.5:c.1788G>A
NM_004737.7:c.1788G>A
NM_133642.5:c.1788G>AMANE SELECT
NP_001349878.1:p.Ala596=
NP_001349880.1:p.Ala596=
NP_001349882.1:p.Ala596=
NP_001365553.1:p.Ala596=
NP_001365554.1:p.Ala596=
NP_001365555.1:p.Ala596=
NP_001365558.1:p.Ala544=
NP_001365559.1:p.Ala395=
NP_004728.1:p.Ala596=
NP_598397.1:p.Ala596=
LRG_856t1:c.1788G>A
LRG_856t2:c.1788G>A
LRG_856:g.642138G>A
LRG_856p1:p.Ala596=
LRG_856p2:p.Ala596=
NC_000022.10:g.33679277C>T
NM_004737.4:c.1788G>A
NP_004728.1:p.(=)
p.Ala596Ala

Links:

dbSNP: rs74550830

NCBI 1000 Genomes Browser:

rs74550830

Molecular consequence:

NM_001378627.1:c.1731-6036G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001378628.1:c.1731-6036G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001378631.1:c.972-6036G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001362949.2:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001362951.2:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001362953.2:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001378624.1:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001378625.1:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001378626.1:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001378629.1:c.1632G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001378630.1:c.1185G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_004737.7:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_133642.5:c.1788G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

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
SCV000513463	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jun 23, 2020)	germline	clinical testing	Citation Link,
SCV000613994	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Nov 16, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003916363	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Dec 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000513463

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Jun 23, 2020)

germline

clinical testing

Citation Link,

SCV000613994

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Nov 16, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003916363

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Dec 1, 2024)

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	9	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV000513463.6

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Athena Diagnostics, SCV000613994.2

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

#	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 CeGaT Center for Human Genetics Tuebingen, SCV003916363.15

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	9	not provided	not provided	clinical testing	not provided

Description

LARGE1: BP4, BP7, BS2

#	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		9	not provided	not provided	not provided

Last Updated: Mar 22, 2025

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