NM_014159.7(SETD2):c.19C>T (p.Gln7Ter) AND Luscan-Lumish syndrome

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Dec 7, 2023
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:: RCV000652616.14

Allele description [Variation Report for NM_014159.7(SETD2):c.19C>T (p.Gln7Ter)]

NM_014159.7(SETD2):c.19C>T (p.Gln7Ter)

Genes:

LOC129936665:ATAC-STARR-seq lymphoblastoid silent region 14306 [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.19C>T (p.Gln7Ter)

HGVS:

NC_000003.12:g.47163906G>A
NG_032091.1:g.5072C>T
NM_001349370.3:c.-98C>T
NM_014159.7:c.19C>TMANE SELECT
NP_054878.5:p.Gln7Ter
NP_054878.5:p.Gln7Ter
LRG_775t1:c.19C>T
LRG_775:g.5072C>T
LRG_775p1:p.Gln7Ter
NC_000003.11:g.47205396G>A
NM_014159.6:c.19C>T
NR_146158.3:n.208C>T

Protein change:

Q7*

Links:

dbSNP: rs541943893

NCBI 1000 Genomes Browser:

rs541943893

Molecular consequence:

NM_001349370.3:c.-98C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_146158.3:n.208C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_014159.7:c.19C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000774487	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001526392	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 2, 2018)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23160955, 25741868
SCV002764552	New York Genome Center	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Uncertain significance (Sep 12, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000774487

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 7, 2023)

germline

clinical testing

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

SCV001526392

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 2, 2018)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV002764552

New York Genome Center

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Uncertain significance
(Sep 12, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	2	not provided	not provided	2	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical 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

Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.

O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, et al.

Science. 2012 Dec 21;338(6114):1619-22. doi: 10.1126/science.1227764. Epub 2012 Nov 15.

PubMed [citation]

PMID:: 23160955
PMCID:: PMC3528801

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000774487.6

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

#	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

From Baylor Genetics, SCV001526392.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been reported in one patient (12736.p1) with autism spectrum disorder and it was inherited from the patient's mother [PMID: 23160955]

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From New York Genome Center, SCV002764552.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided
2	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	1	not provided	not provided		1	not provided	not provided	not provided
2	germline	unknown	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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