NM_030973.4(MED25):c.569C>T (p.Ala190Val) AND Charcot-Marie-Tooth disease type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 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:: RCV000653921.9

Allele description [Variation Report for NM_030973.4(MED25):c.569C>T (p.Ala190Val)]

NM_030973.4(MED25):c.569C>T (p.Ala190Val)

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.569C>T (p.Ala190Val)

HGVS:

NC_000019.10:g.49829829C>T
NG_017091.1:g.16551C>T
NM_001378355.1:c.569C>T
NM_030973.4:c.569C>TMANE SELECT
NP_001365284.1:p.Ala190Val
NP_112235.2:p.Ala190Val
NP_112235.2:p.Ala190Val
LRG_368t1:c.569C>T
LRG_368:g.16551C>T
LRG_368p1:p.Ala190Val
NC_000019.9:g.50333086C>T
NM_030973.3:c.569C>T

Protein change:

A190V

Links:

dbSNP: rs780526739

NCBI 1000 Genomes Browser:

rs780526739

Molecular consequence:

NM_001378355.1:c.569C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_030973.4:c.569C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Charcot-Marie-Tooth disease type 2
Synonyms:: Charcot-Marie-Tooth, Type 2
Identifiers:: MONDO: MONDO:0018993; MedGen: C0270914

Recent activity

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site-specific tyrosine recombinase for chromosome partitioning [Bacillus subtili...
site-specific tyrosine recombinase for chromosome partitioning [Bacillus subtilis subsp. subtilis str. 168]
gi|16078677|ref|NP_389496.1|

Protein
conserved hypothetical protein [Bacillus subtilis subsp. subtilis str. 168]
conserved hypothetical protein [Bacillus subtilis subsp. subtilis str. 168]
gi|16078664|ref|NP_389483.1|

Protein
ribosomal protein S16 (BS17) [Bacillus subtilis subsp. subtilis str. 168]
ribosomal protein S16 (BS17) [Bacillus subtilis subsp. subtilis str. 168]
gi|16078662|ref|NP_389481.1|

Protein
AGENCOURT_77792962 NICHD_XGC_skin_m Xenopus laevis cDNA clone IMAGE:8643796 5', ...
AGENCOURT_77792962 NICHD_XGC_skin_m Xenopus laevis cDNA clone IMAGE:8643796 5', mRNA sequence
gi|95019659|gnl|dbEST|39161892|gb|E 43.1|

Nucleotide
AGENCOURT_74343865 NICHD_XGC_tail_m Xenopus laevis cDNA clone IMAGE:8544840 5', ...
AGENCOURT_74343865 NICHD_XGC_tail_m Xenopus laevis cDNA clone IMAGE:8544840 5', mRNA sequence
gi|92063447|gnl|dbEST|37993492|gb|E 23.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000775811	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000775811

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000775811.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 543225). This variant has not been reported in the literature in individuals affected with MED25-related conditions. This variant is present in population databases (rs780526739, gnomAD 0.007%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 190 of the MED25 protein (p.Ala190Val).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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