NM_002899.5(RBP1):c.387_400del (p.Lys131fs) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 5, 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:: RCV002514775.2

Allele description [Variation Report for NM_002899.5(RBP1):c.387_400del (p.Lys131fs)]

NM_002899.5(RBP1):c.387_400del (p.Lys131fs)

Genes:

COPB2-DT:COPB2 divergent transcript [Gene - HGNC]
RBP1:retinol binding protein 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q23

Genomic location:

Preferred name:

NM_002899.5(RBP1):c.387_400del (p.Lys131fs)

HGVS:

NC_000003.12:g.139538819_139538832del
NG_047073.1:g.5998_6011del
NM_001130992.3:c.387_400del
NM_001130993.3:c.387_400del
NM_001365940.2:c.201_214del
NM_002899.5:c.387_400delMANE SELECT
NP_001124464.1:p.Lys131fs
NP_001124465.1:p.Lys131fs
NP_001352869.1:p.Lys69fs
NP_002890.2:p.Lys131fs
NC_000003.11:g.139257661_139257674del
NM_002899.3:c.387_400delTGGGAAGGAGTTTG

Protein change:

K131fs

Links:

dbSNP: rs587783020

NCBI 1000 Genomes Browser:

rs587783020

Molecular consequence:

NM_001130992.3:c.387_400del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001130993.3:c.387_400del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365940.2:c.201_214del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002899.5:c.387_400del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Related DataSets for GEO Profiles (Select 42688910) (1)
GEO DataSets
RhoGDIbeta depletion effect on breast cancer cell line
RhoGDIbeta depletion effect on breast cancer cell line
Accession: GDS2864

GEO DataSets
Assembly Links for BioProject (Select 323691) (157)
Assembly

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003525672	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 5, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25445212, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003525672

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 5, 2022)

germline

clinical testing

PubMed (2)
[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

Diagnostic application of an extensive gene panel for Leber congenital amaurosis with severe genetic heterogeneity.

Seong MW, Seo SH, Yu YS, Hwang JM, Cho SI, Ra EK, Park H, Lee SJ, Kim JY, Park SS.

J Mol Diagn. 2015 Jan;17(1):100-5. doi: 10.1016/j.jmoldx.2014.09.003. Epub 2014 Oct 24.

PubMed [citation]

PMID:: 25445212

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003525672.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 156390). This premature translational stop signal has been observed in individual(s) with RBP1-related conditions (PMID: 25445212). This variant is present in population databases (rs587783020, gnomAD 0.03%). This sequence change creates a premature translational stop signal (p.Lys131Glyfs*7) in the RBP1 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in RBP1 cause disease.

#	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: Feb 14, 2024

ClinVar

Relating variation to medicine