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NM_001374736.1(DST):c.22975A>T (p.Thr7659Ser) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 10, 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:
RCV002846464.2

Allele description [Variation Report for NM_001374736.1(DST):c.22975A>T (p.Thr7659Ser)]

NM_001374736.1(DST):c.22975A>T (p.Thr7659Ser)

Gene:
DST:dystonin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p12.1
Genomic location:
Preferred name:
NM_001374736.1(DST):c.22975A>T (p.Thr7659Ser)
HGVS:
  • NC_000006.12:g.56463141T>A
  • NG_029322.2:g.496488A>T
  • NM_001144769.5:c.16546A>T
  • NM_001144770.2:c.16132A>T
  • NM_001374722.1:c.22903A>T
  • NM_001374729.1:c.21999+424A>T
  • NM_001374730.1:c.15741+424A>T
  • NM_001374734.1:c.22930A>T
  • NM_001374736.1:c.22975A>TMANE SELECT
  • NM_001386100.1:c.15994A>T
  • NM_015548.5:c.15034A>T
  • NM_183380.4:c.16012A>T
  • NP_001138241.1:p.Thr5516Ser
  • NP_001138242.1:p.Thr5378Ser
  • NP_001361651.1:p.Thr7635Ser
  • NP_001361663.1:p.Thr7644Ser
  • NP_001361665.1:p.Thr7659Ser
  • NP_001373029.1:p.Thr5332Ser
  • NP_056363.2:p.Thr5012Ser
  • NP_899236.1:p.Thr5338Ser
  • NC_000006.11:g.56327939T>A
Protein change:
T5012S
Molecular consequence:
  • NM_001374729.1:c.21999+424A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374730.1:c.15741+424A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001144769.5:c.16546A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001144770.2:c.16132A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374722.1:c.22903A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374734.1:c.22930A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374736.1:c.22975A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386100.1:c.15994A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015548.5:c.15034A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_183380.4:c.16012A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary sensory and autonomic neuropathy type 6
Synonyms:
HSAN VI; Neuropathy, hereditary sensory and autonomic, type VI
Identifiers:
MONDO: MONDO:0013839; MedGen: C3539003; Orphanet: 314381; OMIM: 614653
Name:
Epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency (EBS3)
Synonyms:
Epidermolysis bullosa simplex, autosomal recessive 2; Epidermolysis bullosa simplex due to BP230 deficiency
Identifiers:
MONDO: MONDO:0014180; MedGen: C3809470; Orphanet: 412181; OMIM: 615425

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003220176Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 10, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV003220176.2

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

Description

This variant is not present in population databases (gnomAD no frequency). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with DST-related conditions. This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 5012 of the DST protein (p.Thr5012Ser). The DST gene has multiple clinically relevant transcripts. This variant occurs in alternate transcript NM_015548.4, and corresponds to NM_001723.5:c.*152376A>T in the primary transcript.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024