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NM_014159.7(SETD2):c.6029C>T (p.Thr2010Ile) AND Luscan-Lumish syndrome

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
May 1, 2020
Review status:
criteria provided, conflicting classifications
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:
RCV001227955.9

Allele description [Variation Report for NM_014159.7(SETD2):c.6029C>T (p.Thr2010Ile)]

NM_014159.7(SETD2):c.6029C>T (p.Thr2010Ile)

Gene:
SETD2:SET domain containing 2, histone lysine methyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_014159.7(SETD2):c.6029C>T (p.Thr2010Ile)
HGVS:
  • NC_000003.12:g.47083751G>A
  • NG_032091.1:g.85227C>T
  • NM_001349370.3:c.5897C>T
  • NM_014159.7:c.6029C>TMANE SELECT
  • NP_001336299.1:p.Thr1966Ile
  • NP_054878.5:p.Thr2010Ile
  • LRG_775t1:c.6029C>T
  • LRG_775:g.85227C>T
  • NC_000003.11:g.47125241G>A
  • NM_014159.6:c.6029C>T
  • NR_146158.3:n.6218C>T
Protein change:
T1966I
Links:
dbSNP: rs2041416610
NCBI 1000 Genomes Browser:
rs2041416610
Molecular consequence:
  • NM_001349370.3:c.5897C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014159.7:c.6029C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146158.3:n.6218C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Luscan-Lumish syndrome
Identifiers:
MONDO: MONDO:0014791; MedGen: C4085873; OMIM: 616831

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001400335Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Mar 7, 2020)
germlineclinical testing

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

SCV002025741New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)
Uncertain significance
(May 1, 2020)
inheritedclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedunknown1not providednot provided1not 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001400335.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From New York Genome Center - CSER-NYCKidSeq, SCV002025741.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited c.6029C>T (p.Thr2010Ile) missense variant in exon 12 of 21 of SETD2 has not been reported in affected individuals in the available literature. This variant is not present in gnomAD indicating it is not a common benign variant in the populations represented in this database. In silico predictors suggest this variant is Damaging (Provean; score: -2.57) and Tolerated (SIFT; score: 0.085). Given the conflicting evidence regarding its pathogenicity, the inherited c.6029C>T (p.Thr2010Ile) variant identified in the SETD2 gene is reported as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Feb 20, 2024