NM_000304.4(PMP22):c.34C>T (p.His12Tyr) AND Dejerine-Sottas disease

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 22, 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:: RCV002251247.1

Allele description [Variation Report for NM_000304.4(PMP22):c.34C>T (p.His12Tyr)]

NM_000304.4(PMP22):c.34C>T (p.His12Tyr)

Gene:

PMP22:peripheral myelin protein 22 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p12

Genomic location:

Preferred name:

NM_000304.4(PMP22):c.34C>T (p.His12Tyr)

HGVS:

NC_000017.11:g.15260694G>A
NG_007949.1:g.9634C>T
NM_000304.4:c.34C>TMANE SELECT
NM_001281455.2:c.34C>T
NM_001281456.2:c.34C>T
NM_001330143.2:c.34C>T
NM_153321.3:c.34C>T
NM_153322.3:c.34C>T
NP_000295.1:p.His12Tyr
NP_001268384.1:p.His12Tyr
NP_001268385.1:p.His12Tyr
NP_001317072.1:p.His12Tyr
NP_696996.1:p.His12Tyr
NP_696997.1:p.His12Tyr
LRG_263:g.9634C>T
NC_000017.10:g.15164011G>A

Protein change:

H12Y

Links:

dbSNP: rs2150710219

NCBI 1000 Genomes Browser:

rs2150710219

Molecular consequence:

NM_000304.4:c.34C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281455.2:c.34C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281456.2:c.34C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330143.2:c.34C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153321.3:c.34C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153322.3:c.34C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Dejerine-Sottas disease
Synonyms:: HEREDITARY MOTOR AND SENSORY NEUROPATHY TYPE III; HMSN Type III; Hypertrophic neuropathy of Dejerine-Sottas; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007790; MedGen: C0011195; Orphanet: 64748; OMIM: 145900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002521810	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 22, 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

SCV002521810

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 22, 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	yes	1	not provided	not provided	1	not provided	clinical 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 3billion, SCV002521810.1

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

Description

The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.77; 3Cnet: 0.70). Different missense changes at the same codon (p.His12Arg, p.His12Gln) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000008434, VCV000835185). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Dec 24, 2023

ClinVar

Relating variation to medicine