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NM_014159.7(SETD2):c.500C>T (p.Pro167Leu) AND Luscan-Lumish syndrome

Germline classification:
Benign (2 submissions)
Last evaluated:
Aug 2, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000543864.9

Allele description [Variation Report for NM_014159.7(SETD2):c.500C>T (p.Pro167Leu)]

NM_014159.7(SETD2):c.500C>T (p.Pro167Leu)

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.500C>T (p.Pro167Leu)
HGVS:
  • NC_000003.12:g.47124136G>A
  • NG_032091.1:g.44842C>T
  • NM_001349370.3:c.368C>T
  • NM_014159.7:c.500C>TMANE SELECT
  • NP_001336299.1:p.Pro123Leu
  • NP_054878.5:p.Pro167Leu
  • NP_054878.5:p.Pro167Leu
  • LRG_775t1:c.500C>T
  • LRG_775:g.44842C>T
  • LRG_775p1:p.Pro167Leu
  • NC_000003.11:g.47165626G>A
  • NM_014159.6:c.500C>T
  • NR_146158.3:n.689C>T
Protein change:
P123L
Links:
dbSNP: rs78682369
NCBI 1000 Genomes Browser:
rs78682369
Molecular consequence:
  • NM_001349370.3:c.368C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014159.7:c.500C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146158.3:n.689C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000655750Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Aug 2, 2023)
germlineclinical testing

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

SCV002554250Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Mar 15, 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 providedgermlinenonot 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. 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, SCV000655750.6

#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 Genome-Nilou Lab, SCV002554250.1

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

Last Updated: Jul 7, 2024