NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 15, 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:: RCV001851607.6

Allele description [Variation Report for NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter)]

NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter)

Gene:

DYM:dymeclin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.1

Genomic location:

Preferred name:

NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter)

HGVS:

NC_000018.10:g.49378592A>T
NG_009239.2:g.87142T>A
NM_001353210.3:c.396T>A
NM_001353211.3:c.393T>A
NM_001353212.3:c.393T>A
NM_001353213.3:c.396T>A
NM_001353214.3:c.396T>AMANE SELECT
NM_001353215.3:c.396T>A
NM_001353216.3:c.396T>A
NM_001374428.1:c.396T>A
NM_001374429.1:c.393T>A
NM_001374430.1:c.396T>A
NM_001374431.1:c.396T>A
NM_001374432.1:c.396T>A
NM_001374433.1:c.396T>A
NM_001374434.1:c.396T>A
NM_001374435.1:c.396T>A
NM_001374436.1:c.396T>A
NM_001374437.1:c.396T>A
NM_001374438.1:c.396T>A
NM_001374439.1:c.393T>A
NM_001374440.1:c.193+13001T>A
NM_001374441.1:c.193+13001T>A
NM_001374442.1:c.193+13001T>A
NM_001374443.1:c.193+13001T>A
NM_001374444.1:c.193+13001T>A
NM_017653.6:c.396T>A
NP_001340139.1:p.Tyr132Ter
NP_001340140.1:p.Tyr131Ter
NP_001340141.1:p.Tyr131Ter
NP_001340142.1:p.Tyr132Ter
NP_001340143.1:p.Tyr132Ter
NP_001340144.1:p.Tyr132Ter
NP_001340145.1:p.Tyr132Ter
NP_001361357.1:p.Tyr132Ter
NP_001361358.1:p.Tyr131Ter
NP_001361359.1:p.Tyr132Ter
NP_001361360.1:p.Tyr132Ter
NP_001361361.1:p.Tyr132Ter
NP_001361362.1:p.Tyr132Ter
NP_001361363.1:p.Tyr132Ter
NP_001361364.1:p.Tyr132Ter
NP_001361365.1:p.Tyr132Ter
NP_001361366.1:p.Tyr132Ter
NP_001361367.1:p.Tyr132Ter
NP_001361368.1:p.Tyr131Ter
NP_060123.3:p.Tyr132Ter
NC_000018.9:g.46904962A>T
NM_017653.3:c.396T>A
NM_017653.5:c.396T>A

Protein change:

Y131*; TYR132TER

Links:

OMIM: 607461.0003; dbSNP: rs120074162

NCBI 1000 Genomes Browser:

rs120074162

Molecular consequence:

NM_001374440.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374441.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374442.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374443.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374444.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001353210.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353211.3:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353212.3:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353213.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353214.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353215.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353216.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374428.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374429.1:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374430.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374431.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374432.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374433.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374434.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374435.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374436.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374437.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374438.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374439.1:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_017653.6:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002152740	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 15, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12491225, 12554689, 18996921, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002152740

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 15, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene.

Cohn DH, Ehtesham N, Krakow D, Unger S, Shanske A, Reinker K, Powell BR, Rimoin DL.

Am J Hum Genet. 2003 Feb;72(2):419-28. Epub 2002 Dec 16.

PubMed [citation]

PMID:: 12491225
PMCID:: PMC420018

Mutations in a novel gene Dymeclin (FLJ20071) are responsible for Dyggve-Melchior-Clausen syndrome.

El Ghouzzi V, Dagoneau N, Kinning E, Thauvin-Robinet C, Chemaitilly W, Prost-Squarcioni C, Al-Gazali LI, Verloes A, Le Merrer M, Munnich A, Trembath RC, Cormier-Daire V.

Hum Mol Genet. 2003 Feb 1;12(3):357-64.

PubMed [citation]

PMID:: 12554689

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002152740.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 3186). This premature translational stop signal has been observed in individual(s) with Dyggve-Melchior-Clausen syndrome (PMID: 12491225). This variant is present in population databases (rs120074162, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Tyr132*) in the DYM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DYM are known to be pathogenic (PMID: 12491225, 12554689, 18996921).

#	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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