NM_000350.3(ABCA4):c.6088C>T (p.Arg2030Ter) AND not provided

Germline classification:: Pathogenic (5 submissions)
Last evaluated:: Dec 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:: RCV000085786.15

Allele description [Variation Report for NM_000350.3(ABCA4):c.6088C>T (p.Arg2030Ter)]

NM_000350.3(ABCA4):c.6088C>T (p.Arg2030Ter)

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.6088C>T (p.Arg2030Ter)

Other names:

NM_000350.3(ABCA4):c.6088C>T; p.Arg2030Ter; NP_000341.2:p.(Arg2030Ter)

HGVS:

NC_000001.11:g.94005500G>A
NG_009073.1:g.120650C>T
NG_009073.2:g.120648C>T
NM_000350.3:c.6088C>TMANE SELECT
NM_001425324.1:c.5866C>T
NP_000341.2:p.Arg2030Ter
NP_001412253.1:p.Arg1956Ter
NC_000001.10:g.94471056G>A
NM_000350.2:c.6088C>T

Protein change:

R1956*; ARG2030TER

Links:

OMIM: 601691.0029; dbSNP: rs61751383

NCBI 1000 Genomes Browser:

rs61751383

Molecular consequence:

NM_000350.3:c.6088C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425324.1:c.5866C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Mus musculus spermatogenesis associated 9 (Spata9), transcript varian...
PREDICTED: Mus musculus spermatogenesis associated 9 (Spata9), transcript variant X4, mRNA
gi|1907094649|ref|XM_036158203.1|

Nucleotide
PREDICTED: Rattus norvegicus copine 7 (Cpne7), transcript variant X1, mRNA
PREDICTED: Rattus norvegicus copine 7 (Cpne7), transcript variant X1, mRNA
gi|2678913661|ref|XM_039097880.2|

Nucleotide
PREDICTED: Homo sapiens uncharacterized lncRNA (LOC105372577), transcript varian...
PREDICTED: Homo sapiens uncharacterized lncRNA (LOC105372577), transcript variant X3, ncRNA
gi|2217336745|ref|XR_937392.3|

Nucleotide
Culex quinquefasciatus isolate 47 REC 2018 odorant binding protein 11 (OBP11) ge...
Culex quinquefasciatus isolate 47 REC 2018 odorant binding protein 11 (OBP11) gene, complete cds
gi|2517520302|gb|OP760293.1|

Nucleotide
Pseudomonas mandelii strain IHB B 10205 16S ribosomal RNA gene, partial sequence
Pseudomonas mandelii strain IHB B 10205 16S ribosomal RNA gene, partial sequence
gi|913750938|gb|KR233778.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000117928	Retina International	no classification provided	not provided	not provided	not provided
SCV000490381	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 24, 2023)	germline	clinical testing	Citation Link,
SCV001222421	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 1, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 10958761, 24938718, 25312043, 26780318, 25544989, 28947085, 28492532
SCV001923531	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001954312	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

Description

http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_ABCR:c.6088C>T: SCV000117928

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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	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

Citations

PubMed

Mutations in the ABCA4 (ABCR) gene are the major cause of autosomal recessive cone-rod dystrophy.

Maugeri A, Klevering BJ, Rohrschneider K, Blankenagel A, Brunner HG, Deutman AF, Hoyng CB, Cremers FP.

Am J Hum Genet. 2000 Oct;67(4):960-6. Epub 2000 Aug 24.

PubMed [citation]

PMID:: 10958761
PMCID:: PMC1287897

Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing.

Xu Y, Guan L, Shen T, Zhang J, Xiao X, Jiang H, Li S, Yang J, Jia X, Yin Y, Guo X, Wang J, Zhang Q.

Hum Genet. 2014 Oct;133(10):1255-71. doi: 10.1007/s00439-014-1460-2. Epub 2014 Jun 18.

PubMed [citation]

PMID:: 24938718

See all PubMed Citations (7)

Details of each submission

From Retina International, SCV000117928.1

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

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

From GeneDx, SCV000490381.2

#	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 or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25544989, 26551331, 9973280, 28947085, 29186038, 25525159, 33090715, 35119454, 32619608, 29641573, 23755871, 22589445, 34758253, 30093795, 26780318, 33691693, 33301772, 26247787, 29925512)

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001222421.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This sequence change creates a premature translational stop signal (p.Arg2030*) in the ABCA4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABCA4 are known to be pathogenic (PMID: 10958761, 24938718, 25312043, 26780318). This variant is present in population databases (rs61751383, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with ABCA4-related retinal diseases (PMID: 25544989, 28947085). ClinVar contains an entry for this variant (Variation ID: 7907). For these reasons, this variant has been classified as Pathogenic.

#	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 Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001923531.1

#	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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001954312.1

#	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: Nov 10, 2024

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