NM_020366.4(RPGRIP1):c.1800_1805del (p.Ser601_Leu602del) AND Leber congenital amaurosis 6

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 1, 2022
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:: RCV002467478.1

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.1800_1805del (p.Ser601_Leu602del)]

NM_020366.4(RPGRIP1):c.1800_1805del (p.Ser601_Leu602del)

Gene:

RPGRIP1:RPGR interacting protein 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

14q11.2

Genomic location:

Preferred name:

NM_020366.4(RPGRIP1):c.1800_1805del (p.Ser601_Leu602del)

Other names:

p.Ser601_Leu602del

HGVS:

NC_000014.9:g.21324655_21324660del
NG_008933.1:g.41679_41684del
NG_008933.2:g.49574_49579del
NM_001377523.1:c.688+2651_688+2656del
NM_001377948.1:c.726_731del
NM_001377949.1:c.726_731del
NM_001377950.1:c.688+2651_688+2656del
NM_001377951.1:c.190+2651_190+2656del
NM_020366.4:c.1800_1805delMANE SELECT
NP_001364877.1:p.Ser243_Leu244del
NP_001364878.1:p.Ser243_Leu244del
NP_065099.3:p.Ser601_Leu602del
NC_000014.8:g.21792814_21792819del

Molecular consequence:

NM_001377948.1:c.726_731del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001377949.1:c.726_731del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_020366.4:c.1800_1805del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001377523.1:c.688+2651_688+2656del - intron variant - [Sequence Ontology: SO:0001627]
NM_001377950.1:c.688+2651_688+2656del - intron variant - [Sequence Ontology: SO:0001627]
NM_001377951.1:c.190+2651_190+2656del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Leber congenital amaurosis 6 (LCA6)
Identifiers:: MONDO: MONDO:0013446; MedGen: C1854260; Orphanet: 65; OMIM: 613826

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002762844	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002762844

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 1, 2022)

germline

clinical testing

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

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

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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV002762844.1

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

Description

A heterozygous 6 base pair deletion in Exon 15 of the RPGRIP1 gene that results in the in-frame deletion of amino acids (p.Ser601_Leu602del) was detected. This variant has not been reported in the 1000 genomes, gnomAD and our internal databases. The reference codons are conserved across species. In summary, the variant meets our criteria to be classified as variant of uncertain significance.

#	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: Dec 24, 2022

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