NM_030973.3(MED25):c.556C>T (p.Arg186Trp) AND Basel-Vanagaite-Smirin-Yosef syndrome

Clinical significance:Likely pathogenic (Last evaluated: Feb 14, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000758140.1

Allele description [Variation Report for NM_030973.3(MED25):c.556C>T (p.Arg186Trp)]

NM_030973.3(MED25):c.556C>T (p.Arg186Trp)

Gene:
MED25:mediator complex subunit 25 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.33
Genomic location:
Preferred name:
NM_030973.3(MED25):c.556C>T (p.Arg186Trp)
HGVS:
  • NC_000019.10:g.49829816C>T
  • NG_017091.1:g.16538C>T
  • NM_030973.3:c.556C>T
  • NP_112235.2:p.Arg186Trp
  • LRG_368t1:c.556C>T
  • LRG_368:g.16538C>T
  • LRG_368p1:p.Arg186Trp
  • NC_000019.9:g.50333073C>T
Protein change:
R186W
Links:
dbSNP: rs776291104
NCBI 1000 Genomes Browser:
rs776291104
Molecular consequence:
  • NM_030973.3:c.556C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Basel-Vanagaite-Smirin-Yosef syndrome (BVSYS)
Identifiers:
MONDO: MONDO:0014643; MedGen: C4225323; OMIM: 616449

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000882839Medical Genetics Lab, Policlinico S. Orsola.Malpighicriteria provided, single submitter
Likely pathogenic
(Feb 14, 2019)
paternalclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedpaternalyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Medical Genetics Lab, Policlinico S. Orsola.Malpighi, SCV000882839.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testingnot provided

Description

This is a rare missense variant affecting MED25. Only 2 alleles in gnomAD, allele frequency = 0.00000893 is smaller than 0.0001 threshold for recessive gene MED25. Multiple lines of computational evidence support a deleterious effect on the gene. Patient's phenotype is highly specific for a disease with a single genetic etiology. This variant was detected in trans with a pathogenic variant (p.Pro640LeufsTer81).

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

Last Updated: Oct 8, 2021

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