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NM_030973.4(MED25):c.556C>T (p.Arg186Trp) AND Congenital cataract-microcephaly-nevus flammeus simplex-severe intellectual disability syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 14, 2019
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:
RCV000758140.1

Allele description [Variation Report for NM_030973.4(MED25):c.556C>T (p.Arg186Trp)]

NM_030973.4(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_030973.4(MED25):c.556C>T (p.Arg186Trp)
HGVS:
  • NC_000019.10:g.49829816C>T
  • NG_017091.1:g.16538C>T
  • NM_001378355.1:c.556C>T
  • NM_030973.4:c.556C>TMANE SELECT
  • NP_001365284.1:p.Arg186Trp
  • NP_112235.2:p.Arg186Trp
  • 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
  • NM_030973.3:c.556C>T
Protein change:
R186W
Links:
dbSNP: rs776291104
NCBI 1000 Genomes Browser:
rs776291104
Molecular consequence:
  • NM_001378355.1:c.556C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_030973.4:c.556C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Congenital cataract-microcephaly-nevus flammeus simplex-severe intellectual disability syndrome
Synonyms:
Basel-Vanagaite-Smirin-Yosef syndrome
Identifiers:
MONDO: MONDO:0014643; MedGen: C4225323; OMIM: 616449

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000882839Medical Genetics Lab, Policlinico S. Orsola.Malpighi
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 14, 2019) 		paternalclinical testing

Help

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: Jun 23, 2024