NM_001122769.3(LCA5):c.1062_1068del (p.Cys353_Tyr354insTer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 21, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001858899.4

Allele description [Variation Report for NM_001122769.3(LCA5):c.1062_1068del (p.Cys353_Tyr354insTer)]

NM_001122769.3(LCA5):c.1062_1068del (p.Cys353_Tyr354insTer)

Gene:

LCA5:lebercilin LCA5 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6q14.1

Genomic location:

Preferred name:

NM_001122769.3(LCA5):c.1062_1068del (p.Cys353_Tyr354insTer)

HGVS:

NC_000006.12:g.79491618_79491624del
NG_016011.1:g.50807_50813del
NM_001122769.3:c.1062_1068delMANE SELECT
NM_181714.4:c.1062_1068del
NP_001116241.1:p.Cys353_Tyr354insTer
NP_859065.2:p.Cys353_Tyr354insTer
NC_000006.11:g.80201335_80201341del
NC_000006.11:g.80201335_80201341del
NM_181714.3:c.1062_1068del

Links:

dbSNP: rs1769845495

NCBI 1000 Genomes Browser:

rs1769845495

Molecular consequence:

NM_001122769.3:c.1062_1068del - nonsense - [Sequence Ontology: SO:0001587]
NM_181714.4:c.1062_1068del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002239089	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 21, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 24474277, 32214227, 17546029, 23946133, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002239089

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 21, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of mutations causing inherited retinal degenerations in the israeli and palestinian populations using homozygosity mapping.

Beryozkin A, Zelinger L, Bandah-Rozenfeld D, Shevach E, Harel A, Storm T, Sagi M, Eli D, Merin S, Banin E, Sharon D.

Invest Ophthalmol Vis Sci. 2014 Feb 24;55(2):1149-60. doi: 10.1167/iovs.13-13625.

PubMed [citation]

PMID:: 24474277

First-line exome sequencing in Palestinian and Israeli Arabs with neurological disorders is efficient and facilitates disease gene discovery.

Hengel H, Buchert R, Sturm M, Haack TB, Schelling Y, Mahajnah M, Sharkia R, Azem A, Balousha G, Ghanem Z, Falana M, Balousha O, Ayesh S, Keimer R, Deigendesch W, Zaidan J, Marzouqa H, Bauer P, Schöls L.

Eur J Hum Genet. 2020 Aug;28(8):1034-1043. doi: 10.1038/s41431-020-0609-9. Epub 2020 Mar 25. Erratum in: Eur J Hum Genet. 2022 Feb;30(2):248. doi: 10.1038/s41431-021-00909-7.

PubMed [citation]

PMID:: 32214227
PMCID:: PMC7382450

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002239089.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 810630). This premature translational stop signal has been observed in individual(s) with LCA5-related conditions (PMID: 24474277, 32214227). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr354*) in the LCA5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LCA5 are known to be pathogenic (PMID: 17546029, 23946133).

#	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

Last Updated: Sep 29, 2024

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