NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) AND Age related macular degeneration 2

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Sep 5, 2019
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:: RCV000678513.17

Allele description [Variation Report for NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)]

NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)

Gene:

ABCA4:ATP binding cassette subfamily A member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p22.1

Genomic location:

Preferred name:

NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)

HGVS:

NC_000001.11:g.94008251C>T
NG_009073.1:g.117899G>A
NG_009073.2:g.117897G>A
NM_000350.3:c.5882G>AMANE SELECT
NM_001425324.1:c.5660G>A
NP_000341.2:p.Gly1961Glu
NP_000341.2:p.Gly1961Glu
NP_001412253.1:p.Gly1887Glu
NC_000001.10:g.94473807C>T
NM_000350.2:c.5882G>A
P78363:p.Gly1961Glu

Protein change:

G1887E; GLY1961GLU

Links:

UniProtKB: P78363#VAR_008475; OMIM: 601691.0007; dbSNP: rs1800553

NCBI 1000 Genomes Browser:

rs1800553

Molecular consequence:

NM_000350.3:c.5882G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001425324.1:c.5660G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Age related macular degeneration 2
Synonyms:: MACULAR DEGENERATION, SENILE; MACULOPATHY, AGE-RELATED, 2; MACULOPATHY, AGE-RELATED
Identifiers:: MONDO: MONDO:0007932; MedGen: C3495438; OMIM: 153800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000804584	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	no assertion criteria provided	Pathogenic (Sep 1, 2016)	unknown, inherited	clinical testing
SCV001367829	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 5, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001760045	Genomics England Pilot Project, Genomics England	criteria provided, single submitter (ACGS Guidelines, 2016)	Pathogenic	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000804584

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

no assertion criteria provided

Pathogenic
(Sep 1, 2016)

unknown, inherited

clinical testing

SCV001367829

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 5, 2019)

unknown

clinical testing

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

SCV001760045

Genomics England Pilot Project, Genomics England

criteria provided, single submitter

(ACGS Guidelines, 2016)

Pathogenic

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	1	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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+, SCV000804584.2

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

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001367829.2

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

Description

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: Pm1,PM5,PP3,PP5.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genomics England Pilot Project, Genomics England, SCV001760045.1

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

Last Updated: Jun 9, 2024

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