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NM_001197104.2(KMT2A):c.7354C>G (p.Pro2452Ala) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 12, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001867127.6

Allele description [Variation Report for NM_001197104.2(KMT2A):c.7354C>G (p.Pro2452Ala)]

NM_001197104.2(KMT2A):c.7354C>G (p.Pro2452Ala)

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.7354C>G (p.Pro2452Ala)
Other names:
p.Pro2452Ala
HGVS:
  • NC_000011.10:g.118503246C>G
  • NG_027813.1:g.71757C>G
  • NM_001197104.1:c.7354C>G
  • NM_001197104.2:c.7354C>GMANE SELECT
  • NM_005933.4:c.7345C>G
  • NP_001184033.1:p.Pro2452Ala
  • NP_005924.2:p.Pro2449Ala
  • LRG_613t1:c.7354C>G
  • LRG_613:g.71757C>G
  • NC_000011.9:g.118373961C>G
Protein change:
P2449A
Links:
dbSNP: rs2134391388
NCBI 1000 Genomes Browser:
rs2134391388
Molecular consequence:
  • NM_001197104.2:c.7354C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005933.4:c.7345C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002119828Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 12, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002119828.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt KMT2A protein function. This variant has not been reported in the literature in individuals with KMT2A-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with alanine at codon 2452 of the KMT2A protein (p.Pro2452Ala). The proline residue is moderately conserved and there is a small physicochemical difference between proline and alanine.

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

Last Updated: Sep 29, 2024