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NM_004183.4(BEST1):c.893T>C (p.Phe298Ser) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Aug 7, 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:
RCV000086185.4

Allele description [Variation Report for NM_004183.4(BEST1):c.893T>C (p.Phe298Ser)]

NM_004183.4(BEST1):c.893T>C (p.Phe298Ser)

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.893T>C (p.Phe298Ser)
HGVS:
  • NC_000011.10:g.61959523T>C
  • NG_009033.1:g.14640T>C
  • NM_001139443.2:c.713T>C
  • NM_001300786.2:c.688-369T>C
  • NM_001300787.2:c.713T>C
  • NM_001363591.2:c.575T>C
  • NM_001363592.1:c.1096T>C
  • NM_001363593.2:c.-80T>C
  • NM_004183.4:c.893T>CMANE SELECT
  • NP_001132915.1:p.Phe238Ser
  • NP_001287716.1:p.Phe238Ser
  • NP_001350520.1:p.Phe192Ser
  • NP_001350521.1:p.Leu366=
  • NP_004174.1:p.Phe298Ser
  • NC_000011.9:g.61726995T>C
  • NM_004183.3:c.893T>C
  • NR_134580.2:n.1209T>C
  • O76090:p.Phe298Ser
Protein change:
F192S
Links:
UniProtKB: O76090#VAR_025745; dbSNP: rs281865257
NCBI 1000 Genomes Browser:
rs281865257
Molecular consequence:
  • NM_001363593.2:c.-80T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001300786.2:c.688-369T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001139443.2:c.713T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001300787.2:c.713T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363591.2:c.575T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004183.4:c.893T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134580.2:n.1209T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001363592.1:c.1096T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000118329Retina International
no classification provided
not providednot providednot provided

SCV003440414Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 7, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Description

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providednot providednot providednot providednot providednot provided1not providedliterature only

Citations

PubMed

Ten novel mutations in VMD2 associated with Best macular dystrophy (BMD).

Krämer F, Mohr N, Kellner U, Rudolph G, Weber BH.

Hum Mutat. 2003 Nov;22(5):418.

PubMed [citation]
PMID:
14517959

Clinical and genetic heterogeneity in multifocal vitelliform dystrophy.

Boon CJ, Klevering BJ, den Hollander AI, Zonneveld MN, Theelen T, Cremers FP, Hoyng CB.

Arch Ophthalmol. 2007 Aug;125(8):1100-6.

PubMed [citation]
PMID:
17698758
See all PubMed Citations (4)

Details of each submission

From Retina International, SCV000118329.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003440414.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BEST1 protein function. ClinVar contains an entry for this variant (Variation ID: 99767). This missense change has been observed in individuals with macular dystrophy (PMID: 14517959, 17698758, 23213274). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces phenylalanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 298 of the BEST1 protein (p.Phe298Ser).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024