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

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Oct 1, 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:: RCV000505149.12

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]

Condition(s)

Name:: Retinal dystrophy
Identifiers:: MONDO: MONDO:0019118; MeSH: D058499; MedGen: C0854723; Human Phenotype Ontology: HP:0000556

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000599003	NIHR Bioresource Rare Diseases, University of Cambridge	no assertion criteria provided	Likely pathogenic (Jan 1, 2015)	unknown	research	PubMed (2) [See all records that cite these PMIDs] 9295268, 28041643
SCV001240512	Blueprint Genetics	criteria provided, single submitter (Blueprint Genetics Variant Classification Scheme)	Pathogenic (Aug 17, 2019)	germline	clinical testing	Citation Link,
SCV004706492	Dept Of Ophthalmology, Nagoya University	criteria provided, single submitter (Submitter's publication)	Pathogenic (Oct 1, 2023)	germline	research

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000599003

NIHR Bioresource Rare Diseases, University of Cambridge

no assertion criteria provided

Likely pathogenic
(Jan 1, 2015)

unknown

research

PubMed (2)
[See all records that cite these PMIDs]

SCV001240512

Blueprint Genetics

criteria provided, single submitter

(Blueprint Genetics Variant Classification Scheme)

Pathogenic
(Aug 17, 2019)

germline

clinical testing

Citation Link,

SCV004706492

Dept Of Ophthalmology, Nagoya University

criteria provided, single submitter

(Submitter's publication)

Pathogenic
(Oct 1, 2023)

germline

research

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, research
Admixed American	unknown	yes	1	not provided	not provided	1	not provided	research
European	unknown	yes	1	not provided	not provided	1	not provided	research

Citations

PubMed

Mutation of the Stargardt disease gene (ABCR) in age-related macular degeneration.

Allikmets R, Shroyer NF, Singh N, Seddon JM, Lewis RA, Bernstein PS, Peiffer A, Zabriskie NA, Li Y, Hutchinson A, Dean M, Lupski JR, Leppert M.

Science. 1997 Sep 19;277(5333):1805-7.

PubMed [citation]

PMID:: 9295268

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.

Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, et al.

Am J Hum Genet. 2017 Jan 5;100(1):75-90. doi: 10.1016/j.ajhg.2016.12.003. Epub 2016 Dec 29.

PubMed [citation]

PMID:: 28041643
PMCID:: PMC5223092

Details of each submission

From NIHR Bioresource Rare Diseases, University of Cambridge, SCV000599003.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Admixed American	1	not provided	not provided	research	PubMed (2)
2	European	1	not provided	not provided	research	PubMed (2)

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

From Blueprint Genetics, SCV001240512.1

#	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

From Dept Of Ophthalmology, Nagoya University, SCV004706492.1

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