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NM_014159.7(SETD2):c.3026T>C (p.Met1009Thr) AND Luscan-Lumish syndrome

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jul 12, 2022
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:
RCV001034358.10

Allele description [Variation Report for NM_014159.7(SETD2):c.3026T>C (p.Met1009Thr)]

NM_014159.7(SETD2):c.3026T>C (p.Met1009Thr)

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.3026T>C (p.Met1009Thr)
HGVS:
  • NC_000003.12:g.47121610A>G
  • NG_032091.1:g.47368T>C
  • NM_001349370.3:c.2894T>C
  • NM_014159.7:c.3026T>CMANE SELECT
  • NP_001336299.1:p.Met965Thr
  • NP_054878.5:p.Met1009Thr
  • LRG_775t1:c.3026T>C
  • LRG_775:g.47368T>C
  • NC_000003.11:g.47163100A>G
  • NM_014159.6:c.3026T>C
  • NR_146158.3:n.3215T>C
Protein change:
M1009T
Links:
dbSNP: rs114527197
NCBI 1000 Genomes Browser:
rs114527197
Molecular consequence:
  • NM_001349370.3:c.2894T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014159.7:c.3026T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146158.3:n.3215T>C - 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
SCV001197699Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jul 12, 2022)
germlineclinical testing

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

SCV002098970New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)
Uncertain significance
(Mar 12, 2021)
inheritedclinical testing

Citation Link,

SCV002495954Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Feb 11, 2022)
germlineclinical testing

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

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

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 Invitae, SCV001197699.4

#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, SCV002098970.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV002495954.1

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

Description

SETD2 NM_014159.6 exon 3 p.Met1009Thr (c.3026T>C): This variant has not been reported in the literature but present in 0.01% (7/68030) of European alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/3-47121610-A-G?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:833850). This variant amino acid Threonine (Thr) is present in several species including multiple mammals and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Feb 14, 2024