NM_004183.4(BEST1):c.874G>C (p.Glu292Gln) AND Vitelliform macular dystrophy type 2

Clinical significance:Likely pathogenic (Last evaluated: May 8, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000655874.1

Allele description [Variation Report for NM_004183.4(BEST1):c.874G>C (p.Glu292Gln)]

NM_004183.4(BEST1):c.874G>C (p.Glu292Gln)

Gene:
BEST1:bestrophin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q12.3
Genomic location:
Preferred name:
NM_004183.4(BEST1):c.874G>C (p.Glu292Gln)
HGVS:
  • NC_000011.10:g.61959504G>C
  • NG_009033.1:g.14621G>C
  • NM_001139443.2:c.694G>C
  • NM_001300786.2:c.688-388G>C
  • NM_001300787.2:c.694G>C
  • NM_001363591.2:c.556G>C
  • NM_001363592.1:c.1077G>C
  • NM_001363593.2:c.-99G>C
  • NM_004183.4:c.874G>CMANE SELECT
  • NP_001132915.1:p.Glu232Gln
  • NP_001287716.1:p.Glu232Gln
  • NP_001350520.1:p.Glu186Gln
  • NP_001350521.1:p.Gln359His
  • NP_004174.1:p.Glu292Gln
  • NC_000011.9:g.61726976G>C
  • NM_004183.3:c.874G>C
  • NR_134580.2:n.1190G>C
Protein change:
E186Q
Links:
dbSNP: rs886039311
NCBI 1000 Genomes Browser:
rs886039311
Molecular consequence:
  • NM_001363593.2:c.-99G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001300786.2:c.688-388G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001139443.2:c.694G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001300787.2:c.694G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363591.2:c.556G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363592.1:c.1077G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004183.4:c.874G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134580.2:n.1190G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Vitelliform macular dystrophy type 2 (VMD2)
Synonyms:
VITELLIFORM MACULAR DYSTROPHY, EARLY-ONSET; VITELLIFORM MACULAR DYSTROPHY, JUVENILE-ONSET; Best disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007931; MedGen: C2745945; Orphanet: 1243; OMIM: 153700

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000747140MAGI'S LAB - Medical Genetics Laboratory, MAGI GROUPcriteria provided, single submitter
Likely pathogenic
(May 8, 2018)
paternalclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Caucasianpaternalyes1not providednot providednot providednot providedclinical 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 MAGI'S LAB - Medical Genetics Laboratory, MAGI GROUP, SCV000747140.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedclinical testing PubMed (1)

Description

The p.(Glu292Gln) variant in BEST1 has been identified in a proband and his father both affected by Best vitelliform macular dystrophy (BVMD). Application of ACMG guidelines: PM2, absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium; PM5, novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before; PP1, cosegregation with disease in multiple affected family members in a gene definitely known to cause the disease. PP3, multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). In summary, the p.(Glu292Gln) variant meets the ACMG criteria to be classified as likely pathogenic.

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

Last Updated: May 11, 2020

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