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NM_003482.3(KMT2D):c.7670C>T (p.Pro2557Leu)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Sep 30, 2021)
Last evaluated:
Nov 27, 2020
Accession:
VCV000094250.10
Variation ID:
94250
Description:
single nucleotide variant
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NM_003482.3(KMT2D):c.7670C>T (p.Pro2557Leu)

Allele ID
100150
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.12
Genomic location
12: 49040100 (GRCh38) GRCh38 UCSC
12: 49433883 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.49433883G>A
NC_000012.12:g.49040100G>A
NG_027827.1:g.20225C>T
... more HGVS
Protein change
P2557L
Other names
-
Canonical SPDI
NC_000012.12:49040099:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00859 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00824
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00925
1000 Genomes Project 0.00859
The Genome Aggregation Database (gnomAD) 0.00886
Trans-Omics for Precision Medicine (TOPMed) 0.00894
Exome Aggregation Consortium (ExAC) 0.00849
Links
ClinGen: CA147707
UniProtKB: O14686#VAR_064374
dbSNP: rs189888707
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 7 criteria provided, multiple submitters, no conflicts Jun 5, 2017 RCV000080213.11
Benign 1 criteria provided, single submitter Nov 27, 2020 RCV000351079.6
Benign 1 criteria provided, single submitter Sep 14, 2016 RCV000425546.4
Benign 1 criteria provided, single submitter Sep 27, 2019 RCV001001867.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KMT2D Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1709 1723

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000309631.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Sep 14, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000510696.1
Submitted: (Feb 17, 2017)
Evidence details
Benign
(Jun 05, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000728620.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Sep 27, 2019)
criteria provided, single submitter
Method: clinical testing
Kabuki syndrome 1
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001159584.2
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Nov 27, 2020)
criteria provided, single submitter
Method: clinical testing
Kabuki syndrome
Allele origin: germline
Invitae
Accession: SCV000636672.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 21, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000193474.1
Submitted: (Sep 11, 2014)
Evidence details
Benign
(Dec 22, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000112108.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959995.1
Submitted: (Sep 30, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001973575.1
Submitted: (Sep 21, 2021)
Evidence details
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000085590.1
Submitted: (May 29, 2014)
Comment:
Please see associated publication for description of ethnicities
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KMT2D - - - -

Text-mined citations for rs189888707...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 16, 2021