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NM_001042681.2(RERE):c.3466G>T (p.Gly1156Trp) AND Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 15, 2020
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:
RCV001267826.2

Allele description [Variation Report for NM_001042681.2(RERE):c.3466G>T (p.Gly1156Trp)]

NM_001042681.2(RERE):c.3466G>T (p.Gly1156Trp)

Gene:
RERE:arginine-glutamic acid dipeptide repeats [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.23
Genomic location:
Preferred name:
NM_001042681.2(RERE):c.3466G>T (p.Gly1156Trp)
HGVS:
  • NC_000001.11:g.8359916C>A
  • NG_047035.1:g.462776G>T
  • NM_001042681.2:c.3466G>TMANE SELECT
  • NM_001042682.2:c.1804G>T
  • NM_012102.4:c.3466G>T
  • NP_001036146.1:p.Gly1156Trp
  • NP_001036147.1:p.Gly602Trp
  • NP_036234.3:p.Gly1156Trp
  • NC_000001.10:g.8419976C>A
Protein change:
G1156W
Links:
dbSNP: rs766951273
NCBI 1000 Genomes Browser:
rs766951273
Molecular consequence:
  • NM_001042681.2:c.3466G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042682.2:c.1804G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_012102.4:c.3466G>T - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
Unknown function
Observations:
1

Condition(s)

Name:
Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH)
Identifiers:
MONDO: MONDO:0014857; MedGen: C4310772; OMIM: 616975

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001445999Breda Genetics srl
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 15, 2020) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions.

Fregeau B, Kim BJ, Hernández-García A, Jordan VK, Cho MT, Schnur RE, Monaghan KG, Juusola J, Rosenfeld JA, Bhoj E, Zackai EH, Sacharow S, Barañano K, Bosch DGM, de Vries BBA, Lindstrom K, Schroeder A, James P, Kulch P, Lalani SR, van Haelst MM, van Gassen KLI, et al.

Am J Hum Genet. 2016 May 5;98(5):963-970. doi: 10.1016/j.ajhg.2016.03.002. Epub 2016 Apr 14.

PubMed [citation]
PMID:
27087320
PMCID:
PMC4863473

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 Breda Genetics srl, SCV001445999.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (2)

Description

The variant c.3466G>T (p.Gly1156Trp) in the RERE gene has not been reported in dbSNP, gnomAD, 1000 Genomes, NHLI Exome Sequencing Project (ESP) or ClinVar. The nucleotide position is highly conserved across 35 mammalian species (GERP RS: 5.56). In silico analysis indicates that the variant might be damaging. Another de novo pathogenic missense variant, affecting the same nucleotide position, c.3466G>A (p.Gly1156Arg), has been reported by Fregeau et al. (2016) in a child with intrauterine growth retardation, global developmental delay, mild spastic quadriparesis, dysarthric speech, swallowing difficulties, bilateral optic colobomas and other eye abnormalities, mild sensorineural hearing loss, and brain MRI abnormalities (PMID: 27087320). Based on ACMG variant interpretation guidelines, we classify this variant as uncertain. However, based on the aforementioned evidence, there is a given likelihood that the variant may actually be pathogenic, even if we cannot exclude that it is a rare benign variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 23, 2022