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NM_000304.4(PMP22):c.353C>T (p.Thr118Met) AND Tip-toe gait

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 5, 2021
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:
RCV001507314.11

Allele description [Variation Report for NM_000304.4(PMP22):c.353C>T (p.Thr118Met)]

NM_000304.4(PMP22):c.353C>T (p.Thr118Met)

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.353C>T (p.Thr118Met)
HGVS:
  • NC_000017.11:g.15231047G>A
  • NG_007949.1:g.39281C>T
  • NM_000304.4:c.353C>TMANE SELECT
  • NM_001281455.2:c.353C>T
  • NM_001281456.2:c.353C>T
  • NM_153321.3:c.353C>T
  • NM_153322.3:c.353C>T
  • NP_000295.1:p.Thr118Met
  • NP_001268384.1:p.Thr118Met
  • NP_001268385.1:p.Thr118Met
  • NP_696996.1:p.Thr118Met
  • NP_696997.1:p.Thr118Met
  • LRG_263t1:c.353C>T
  • LRG_263:g.39281C>T
  • NC_000017.10:g.15134364G>A
  • NM_000304.2:c.353C>T
  • NM_000304.3:c.353C>T
  • NR_104017.2:n.448C>T
  • NR_104018.2:n.348C>T
  • Q01453:p.Thr118Met
  • p.T118M
Protein change:
T118M; THR118MET
Links:
UniProtKB: Q01453#VAR_006375; OMIM: 601097.0005; dbSNP: rs104894619
NCBI 1000 Genomes Browser:
rs104894619
Molecular consequence:
  • NM_000304.4:c.353C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281455.2:c.353C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281456.2:c.353C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_153321.3:c.353C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_153322.3:c.353C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104017.2:n.448C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104018.2:n.348C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Tip-toe gait
Synonyms:
Toe walking
Identifiers:
MedGen: C0427144; Human Phenotype Ontology: HP:0030051

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001712107Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 5, 2021)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

NGS-Panel Diagnosis Developed for the Differential Diagnosis of Idiopathic Toe Walking and Its Application for the Investigation of Possible Genetic Causes for the Gait Anomaly.

Pomarino D, Emelina A, Heidrich J, Rostásy K, Schirmer S, Schönfeldt JO, Thren A, Wagner F, Thren JR, Berger N.

Glob Med Genet. 2023 Jun;10(2):63-71. doi: 10.1055/s-0043-57230.

PubMed [citation]
PMID:
37091313
PMCID:
PMC10121371

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 Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino, SCV001712107.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testing PubMed (2)
2not providednot providednot providedclinical testing PubMed (2)

Description

The heterozygous variant c.353C> T p. (Thr118Met) was detected in the PMP22 gene [dbSNP rs104894619; frequency T = 0.468% (ExAC)]. In the literature [Shy (2006) Ann Neurol 59: 358; Keckarevic-Markovic (2009) J Peripher Nerv Syst 14: 125; Russo (2011) Neuromuscul Disord 21: 106 and Ho (2018) Case Rep Genet 2018: 2618071] this variant is associated with hereditary neuropathies. However, the authors refer to numerous older studies in which it is controversially discussed and in some cases it is assigned an unclear clinical effect up to and including classification as a non-pathological polymorphism. These very inconsistent and controversial classifications are reflected in the databases ClinVar [4x pathogenic, 13x VUS, 3x likely / benign] and LOVD [7x pathogenic, 5x VUS, 2x likely benign]. A "reduced penetrance" [Russo (2011) Neuromuscul Disord 21: 106] of the proven variant is being discussed, since it was also demonstrated in control groups of the studies. In addition, a partial loss of function was observed for the protein affected by the variant depending on the genotype [Shy (2006) Ann Neurol 59: 358]. Modulating effects due to variants in other genes cannot be ruled out either. Hereditary motor sensory neuropathy (HMSN), also known as Charcot-Marie-Tooth Disease (CMT), is the most commonly inherited peripheral polyneuropathy. It constitutes a group of inherited, progressive, motor and sensory peripheral nerve disorders with properties of demyelination, axonal degeneration, or both. It is classified by clinical characteristics, modes of inheritance, electrophysiologic features, metabolic defects, and specific gene markers. Our patients all walk on tiptoe, so they show similar symptoms. When we genetically test them with our toe walking panel, we find that around 90 per cent of them have a genetic variant that explains their toe walking. These can be assigned, for example, to the area of myopathies (such as variants of the COL6A3 gene), the area of hereditary neuropathies (such as variants of the KMT2C gene) or the area of metabolic diseases (such as variants of the PYGM gene). In a smaller group of patients with almost identical symptoms, no abnormality is found in the genes of our panel, but spastic paraplegia can be detected. In another small group of our toe walkers, no abnormalities can be detected in the genes analysed in our toe walking panel, nor do they suffer from spastic paraplegia, as is also the case with healthy children. In contrast to these, however, they show a tiptoe gait. These patients suffer from infantile cerebral palsy, in which toe walking can also be observed.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided
2unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024