NM_001197104.2(KMT2A):c.3460C>T (p.Arg1154Trp) AND Wiedemann-Steiner syndrome

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Nov 10, 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:: RCV001007914.5

Allele description [Variation Report for NM_001197104.2(KMT2A):c.3460C>T (p.Arg1154Trp)]

NM_001197104.2(KMT2A):c.3460C>T (p.Arg1154Trp)

Gene:

KMT2A:lysine methyltransferase 2A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001197104.2(KMT2A):c.3460C>T (p.Arg1154Trp)

HGVS:

NC_000011.10:g.118478092C>T
NG_027813.1:g.46603C>T
NM_001197104.2:c.3460C>TMANE SELECT
NM_005933.4:c.3460C>T
NP_001184033.1:p.Arg1154Trp
NP_001184033.1:p.Arg1154Trp
NP_005924.2:p.Arg1154Trp
LRG_613t1:c.3460C>T
LRG_613:g.46603C>T
LRG_613p1:p.Arg1154Trp
NC_000011.9:g.118348807C>T
NM_001197104.1:c.3460C>T
NM_005933.3:c.3460C>T

Protein change:

R1154W

Links:

dbSNP: rs1555038090

NCBI 1000 Genomes Browser:

rs1555038090

Molecular consequence:

NM_001197104.2:c.3460C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005933.4:c.3460C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Wiedemann-Steiner syndrome (WDSTS)
Synonyms:: Growth deficiency and mental retardation with facial dysmorphism
Identifiers:: MONDO: MONDO:0011518; MedGen: C1854630; OMIM: 605130

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001167623	Genomic Medicine Lab, University of California San Francisco - CSER	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 10, 2019)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003806871	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 29, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004102703	Daryl Scott Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 10, 2023)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005045322	Department of Pediatrics, Taizhou Central Hospital, Taizhou University Hospital	no assertion criteria provided	Pathogenic (Feb 1, 2024)	de novo	clinical testing

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing
Asia	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Genomic Medicine Lab, University of California San Francisco - CSER, SCV001167623.1

#	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	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV003806871.1

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

Description

ACMG classification criteria: PS3 supporting, PS4 moderated, PM2 moderated, PM6 moderated, PP1 supporting, PP3 supporting

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

From Daryl Scott Lab, Baylor College of Medicine, SCV004102703.1

#	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	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Department of Pediatrics, Taizhou Central Hospital, Taizhou University Hospital, SCV005045322.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Asia	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	de novo	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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