NM_014159.7(SETD2):c.3097A>G (p.Thr1033Ala) AND Luscan-Lumish syndrome

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Apr 24, 2024
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:: RCV000546373.12

Allele description [Variation Report for NM_014159.7(SETD2):c.3097A>G (p.Thr1033Ala)]

NM_014159.7(SETD2):c.3097A>G (p.Thr1033Ala)

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.3097A>G (p.Thr1033Ala)

HGVS:

NC_000003.12:g.47121539T>C
NG_032091.1:g.47439A>G
NM_001349370.3:c.2965A>G
NM_014159.7:c.3097A>GMANE SELECT
NP_001336299.1:p.Thr989Ala
NP_054878.5:p.Thr1033Ala
NP_054878.5:p.Thr1033Ala
LRG_775t1:c.3097A>G
LRG_775:g.47439A>G
LRG_775p1:p.Thr1033Ala
NC_000003.11:g.47163029T>C
NM_014159.6:c.3097A>G
NR_146158.3:n.3286A>G

Protein change:

T1033A

Links:

dbSNP: rs145759179

NCBI 1000 Genomes Browser:

rs145759179

Molecular consequence:

NM_001349370.3:c.2965A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_014159.7:c.3097A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_146158.3:n.3286A>G - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000655730	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Apr 24, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002553692	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Mar 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000655730

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Apr 24, 2024)

germline

clinical testing

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

SCV002553692

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Mar 15, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000655730.7

#	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 Genome-Nilou Lab, SCV002553692.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 22, 2025

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