ClinVar Miner

Submissions for variant NM_000350.3(ABCA4):c.3602T>G (p.Leu1201Arg) (rs61750126)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000176456 SCV000228115 benign not specified 2015-03-05 criteria provided, single submitter clinical testing
Institute of Human Genetics, Univ. Regensburg,Univ. Regensburg RCV000408567 SCV000281871 likely pathogenic Stargardt disease 1 2016-01-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000343774 SCV000359391 likely benign Cone-Rod Dystrophy, Recessive 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000401597 SCV000359392 likely benign Macular degeneration 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000308786 SCV000359393 likely benign Stargardt Disease, Recessive 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000340328 SCV000359394 likely benign Retinitis Pigmentosa, Recessive 2016-06-14 criteria provided, single submitter clinical testing
Mendelics RCV000408567 SCV001135348 likely benign Stargardt disease 1 2019-05-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001096421 SCV001252629 likely benign ABCA4-Related Disorders 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Invitae RCV000085583 SCV001729889 benign not provided 2020-12-02 criteria provided, single submitter clinical testing
GeneDx RCV000085583 SCV001880968 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 28559085, 20647261, 29925512, 25066811, 24011517, 23982839, 27884173, 9973280, 25097241, 16123440, 19074458, 20981092)
OMIM RCV000008361 SCV000028569 pathogenic Cone-rod dystrophy 3 2003-06-01 no assertion criteria provided literature only
Retina International RCV000085583 SCV000117721 not provided not provided no assertion provided not provided
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000176456 SCV001553447 benign not specified no assertion criteria provided clinical testing The ABCA4 p.Leu1201Arg variant was identified in 19 of 988 proband chromosomes (frequency: 0.019) from individuals or families with Stargardt disease and cone-rod dystrophy (Schulz_2017_PMID:28118664; Utz_2013_PMID:24011517; Zernant_2014_PMID:25066811; Fishman_2003_PMID:12796258). The variant was identified in dbSNP (ID: rs61750126), ClinVar (classified as benign by EGL Genetics, likely benign by Illumina and likely pathogenic by Institute of Human Genetics, Univ. Regensburg) and LOVD 3.0 (classified as a VUS and likely benign). The variant was also identified in control databases in 2402 of 266312 chromosomes (114 homozygous) at a frequency of 0.009019 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 2219 of 23326 chromosomes (freq: 0.09513), Other in 32 of 6916 chromosomes (freq: 0.004627), Latino in 133 of 34270 chromosomes (freq: 0.003881), European (non-Finnish) in 16 of 120738 chromosomes (freq: 0.000133) and South Asian in 2 of 28188 chromosomes (freq: 0.000071), while the variant was not observed in the Ashkenazi Jewish, East Asian or European (Finnish) populations. The p.Leu1201 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Clinical Genetics,Academic Medical Center RCV000085583 SCV001925438 likely benign not provided no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000176456 SCV001951648 benign not specified no assertion criteria provided clinical testing

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