Global Variome shared LOVD
KMT2D (lysine (K)-specific methyltransferase 2D)
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Unique variants in the KMT2D gene
The variants shown are described using the NM_003482.3 transcript reference sequence.
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Reported
: The number of times this variant has been reported in the database.
Exon
: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
DNA change (cDNA)
: description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.
RNA change
: description of variant at RNA level (following HGVS recommendations).
r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription
Protein
: description of variant at protein level (following HGVS recommendations).
p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced
Classification method
: The method used for the clinical classification of this variant.
All options:
ACMG
ACGS
EAHAD-CFDB
ENIGMA
InSiGHT
kConFab
other
Clinical classification
: Clinical classification of variant, preferably based on standardised criteria (e.g. ACMG), directed on the clinical consequences as published/submitted, indicated using an enriched system including inheritance: e.g. pathogenic, pathogenic (dominant), pathogenic (recessive), pathogenic (!), pathogenic (maternal), pathogenic (paternal). Standard inheritance is covered by dominant/recessive, sex-linked and imprinting by maternal/paternal. A '!' warns for exceptional circumstances to be explained in the 'Remarks' field (low penetrance, variants pathogenic in heterozygous state only, hypomorphic/hypermorphic variants, protective variants, etc.). Non-disease consequences (e.g. drug metabolism (pharmacogenetics), risk factor, blood group, tasting bitter) are indicated using additions to the benign classification; benign (dominant), benign (recessive), benign (!), etc. The value 'association' is used for variants associated with a phenotype and 'NA' for variants from in vitro/in silico records. NOTE: classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional.
All options:
pathogenic
pathogenic (dominant)
pathogenic (recessive)
pathogenic (!)
pathogenic (maternal)
pathogenic (paternal)
likely pathogenic
likely pathogenic (dominant)
likely pathogenic (recessive)
likely pathogenic (!)
likely pathogenic (maternal)
likely pathogenic (paternal)
VUS
VUS (!)
likely benign
likely benign (dominant)
likely benign (recessive)
likely benign (!)
likely benign (maternal)
likely benign (paternal)
benign
benign (dominant)
benign (recessive)
benign (!)
benign (maternal)
benign (paternal)
association
unclassified
NA
DNA change (genomic) (hg19)
: HGVS description of variant at DNA level, based on the genomic (chromosomal) DNA reference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
DNA change (hg38)
: HGVS description of variant at DNA level, based on the hg38 genomic (chromosomal) eference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
Published as
: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G)
ISCN
: description of the variant according to ISCN nomenclature
DB-ID
: database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro
Variant remarks
: remarks regarding variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
Reference
: publication describing the variant submitted, incl. links to OMIM, PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"
ClinVar ID
: ID of variant in ClinVar database
dbSNP ID
: the dbSNP ID
Origin
: Origin of variant/record: Germline = in all cells, De novo = in all cells, but not in either parent, Germline/De novo (untested) = in all cells, parents not tested (use only when De novo is likely, e.g. isolated/sporadic cases with dominant disease), Somatic = present in a subset of cells, but not in either parent, Uniparental disomy = from parental disomy (maternal or paternal), CLASSIFICATION record = submitter only sharing variant classification (note another report may share Individual data), SUMMARY record = master summary record from curator (may link to another database), In vitro (cloned) = data resulting from in vitro functional assays, animal model = data from animal model, Artefact = false positive variant call, DUPLICATE record = variant already described on another chromosome (e.g. unbalanced translocation, duplicating transposition, 2nd fusion transcript, etc.)
All options:
Germline
De novo
Germline/De novo (untested)
Somatic
Uniparental disomy
Uniparental disomy, maternal allele
Uniparental disomy, paternal allele
CLASSIFICATION record
SUMMARY record
In vitro (cloned)
In silico
animal model
Artefact
DUPLICATE record
Unknown
Not applicable
Segregation
: Indicates whether the variant segregates with the phenotype (yes), does not segregate with the phenotype (no) or segregation is unknown (?)
All options:
? = unknown
yes = segregates with phenotype
no = does not segregate with phenotype
- = not applicable
Frequency
: frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested)
Re-site
: restriction enzyme recognition site created (+) or destroyed (-); e.g. BglII+, BamHI-
VIP
: variant VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator. NOTE: to get VIP status ask the curator.
Methylation
: result of methylation test; GOM (gain of methylation), LOM (loss of methylation), 30% (30% methylated). NOTE: when several tests were done mention the method as well (e.g. MS-PCR 75%)
How to query this table
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Operator
Column type
Example
Matches
Text
Arg
all entries containing 'Arg'
space
Text
Arg Ser
all entries containing 'Arg' and 'Ser'
|
Text
Arg|Ser
all entries containing 'Arg' or 'Ser'
!
Text
!fs
all entries not containing 'fs'
^
Text
^p.(Arg
all entries beginning with 'p.(Arg'
$
Text
Ser)$
all entries ending with 'Ser)'
=""
Text
=""
all entries with this field empty
=""
Text
="p.0"
all entries exactly matching 'p.0'
!=""
Text
!=""
all entries with this field not empty
!=""
Text
!="p.0"
all entries not exactly matching 'p.0?'
combination
Text
*|Ter !fs
all entries containing '*' or 'Ter' but not containing 'fs'
Date
2020
all entries matching the year 2020
|
Date
2020-03|2020-04
all entries matching March or April, 2020
!
Date
!2020-03
all entries not matching March, 2020
<
Date
<2020
all entries before the year 2020
<=
Date
<=2020-06
all entries in or before June, 2020
>
Date
>2020-06
all entries after June, 2020
>=
Date
>=2020-06-15
all entries on or after June 15th, 2020
combination
Date
2019|2020 <2020-03
all entries in 2019 or 2020, and before March, 2020
Numeric
23
all entries exactly matching 23
|
Numeric
23|24
all entries exactly matching 23 or 24
!
Numeric
!23
all entries not exactly matching 23
<
Numeric
<23
all entries lower than 23
<=
Numeric
<=23
all entries lower than, or equal to, 23
>
Numeric
>23
all entries higher than 23
>=
Numeric
>=23
all entries higher than, or equal to, 23
combination
Numeric
>=20 <30 !23
all entries with values from 20 to 29, but not equal to 23
Some more advanced examples:
Example
Matches
Asian
all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian
all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian
all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"
all entries containing 'South Asian', but not containing 'South East Asian'
To sort on a certain column, click on the column header or on the arrows. If that column is already selected to sort on, the sort order will be swapped. The column currently sorted on has a darker blue background color than the other columns. The up and down arrows next to the column name indicate the current sorting direction. When sorting on any field other than the default, LOVD will sort secondarily on the default sort column.
938 entries on 10 pages. Showing entries 1 - 100.
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Effect
Reported
Exon
DNA change (cDNA)
RNA change
Protein
Classification method
Clinical classification
DNA change (genomic) (hg19)
DNA change (hg38)
Published as
ISCN
DB-ID
Variant remarks
Reference
ClinVar ID
dbSNP ID
Origin
Segregation
Frequency
Re-site
VIP
Methylation
Owner
+/.
1
_1_54_
c.1_*2805{0}
r.0
p.0
-
pathogenic (dominant)
g.(?_49412758)_(49449107_?)del
g.(?_49018975)_(49055324_?)del
del gene
-
KMT2D_000969
whole gene deletion, 0.10-0.20 somatic mosaicism
PubMed: Banka 2013
-
-
Somatic
-
-
-
-
-
Johan den Dunnen
+/.
1
(41i_42i)_54_
c.(13839+1_14000-1)_*2805{0}
r.(?)
p.?
-
pathogenic (dominant)
g.(?_4941275)_(49423260_49424383)del
g.(?_49018975)_(49029477_49030600)del
del ex43-54
-
KMT2D_000968
-
PubMed: Banka 2013
-
-
Germline/De novo (untested)
-
-
-
-
-
Johan den Dunnen
+/.
1
2
c.96C>G
r.(?)
p.(Asp32Glu)
-
pathogenic
g.49448763G>C
g.49054980G>C
96C>G, Asp32Glu
-
KMT2D_000535
-
PubMed: Liu 2015
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
-?/.
1
-
c.163C>T
r.(?)
p.(Pro55Ser)
-
likely benign
g.49448696G>A
g.49054913G>A
KMT2D(NM_003482.3):c.163C>T (p.(Pro55Ser))
-
KMT2D_000831
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
+/.
4
2
c.166C>T
r.(?)
p.(Gln56*)
-
pathogenic, pathogenic (dominant)
g.49448693G>A
g.49054910G>A
166C>T, Gln56*
-
KMT2D_000534
inherited from affected parent
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
Germline
yes, ?
-
-
-
-
Vincent Gatinois
,
Nina Bögershausen
+/.
1
2i
c.177-2A>C
r.177_400del
p.Ser59Argfs*86
-
pathogenic
g.49448536T>G
g.49054753T>G
r.177_400del224
-
KMT2D_000008
-
PubMed: Micale 2014
-
-
De novo
-
-
-
-
-
B. Augello
+/.
2
2i
c.177-2A>G
r.spl
p.?
-
pathogenic, pathogenic (dominant)
g.49448536T>C
g.49054753T>C
177-2A>G, (?)
-
KMT2D_000533
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
Germline
?, yes
-
-
-
-
Vincent Gatinois
,
Nina Bögershausen
?/.
1
-
c.206G>C
r.(?)
p.(Cys69Ser)
-
VUS
g.49448505C>G
-
KMT2D(NM_003482.3):c.206G>C (p.C69S)
-
KMT2D_000911
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
+?/.
1
-
c.207T>A
r.(?)
p.(Cys69Ter)
-
likely pathogenic
g.49448504A>T
g.49054721A>T
KMT2D(NM_003482.3):c.207T>A (p.(Cys69Ter))
-
KMT2D_000830
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-/., -?/.
5
3
c.248G>A
r.(?)
p.(Arg83Gln)
-
benign, likely benign
g.49448463C>T
g.49054680C>T
KMT2D(NM_003482.3):c.248G>A (p.R83Q)
-
KMT2D_000105
VKGL data sharing initiative Nederland, 103 heterozygous;
Clinindb (India)
,
1 more item
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs55865069
CLASSIFICATION record, Germline
-
103/2795 individuals, up to 0.06, 4/2795 individuals
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_Nijmegen
,
Mohammed Faruq
,
Andreas Laner
+/.
1
3
c.303del
r.(?)
p.(Ser102Alafs*28)
-
pathogenic (dominant)
g.49448413del
g.49054630del
303delG
-
KMT2D_000985
-
PubMed: Lindsley 2016
-
-
Unknown
-
-
-
-
-
Johan den Dunnen
+/.
1
-
c.303dup
r.(?)
p.(Ser102GlufsTer6)
-
pathogenic
g.49448413dup
g.49054630dup
KMT2D(NM_003482.3):c.303dupG (p.S102Efs*6)
-
KMT2D_000719
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_VUmc
?/.
1
3
c.346T>C
r.(?)
p.(Ser116Pro)
-
VUS
g.49448365A>G
g.49054582A>G
-
-
KMT2D_000007
-
PubMed: Micale 2014
-
-
Germline
?
-
-
-
-
B. Augello
+/.
1
3i
c.400+1G>A
r.177_400del
p.Ser59Argfs*86
-
pathogenic
g.49448310C>T
g.49054527C>T
-
-
KMT2D_000004
-
PubMed: Micale 2014
-
-
Unknown
?
-
-
-
-
B. Augello
+/.
2
3i
c.400+2T>C
r.spl
p.?
-
pathogenic (dominant), pathogenic
g.49448309A>G
g.49054526A>G
400+2T>C, (?)
-
KMT2D_000532
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
Germline
yes, ?
-
-
-
-
Nina Bögershausen
,
Vincent Gatinois
+/.
1
3i
c.401-3A>G
r.400_401insag
p.Gly134Glufs*75
-
pathogenic
g.49448202T>C
g.49054419T>C
-
-
KMT2D_000005
-
PubMed: Micale 2014
-
-
De novo
-
-
-
-
-
B. Augello
?/.
1
-
c.444C>T
r.(?)
p.(Gly148=)
-
VUS
g.49448156G>A
g.49054373G>A
KMT2D(NM_003482.3):c.444C>T (p.G148=)
-
KMT2D_000698
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
4
c.472del
r.(?)
p.(Cys158Valfs*50)
-
pathogenic
g.49448128del
g.49054345del
472delT, Cys158ValfsX50
-
KMT2D_000531
-
PubMed: Micale 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
-?/.
1
-
c.507A>C
r.(?)
p.(Ser169=)
-
likely benign
g.49448093T>G
g.49054310T>G
KMT2D(NM_003482.3):c.507A>C (p.S169=)
-
KMT2D_000861
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
4
c.509A>T
r.(?)
p.(Gln170Leu)
-
pathogenic
g.49448091T>A
g.49054308T>A
509A>T, ?
-
KMT2D_000530
-
PubMed: Makrythanasis 2013
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+/.
1
4
c.510G>A
r.(?)
p.(=)
-
pathogenic
g.49448090C>T
g.49054307C>T
510G>A, ?
-
KMT2D_000529
-
PubMed: Makrythanasis 2013
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
-/., +/.
2
4
c.510G>C
r.(?)
p.(Gln170His)
-
benign, pathogenic
g.49448090C>G
g.49054307C>G
510G>C, ?
-
KMT2D_000006
-
PubMed: Micale 2014
,
PubMed: Makrythanasis 2013
-
-
Germline
?, yes
-
-
-
-
B. Augello
,
Vincent Gatinois
+/.
1
4i
c.510+1G>A
r.spl
p.?
-
pathogenic
g.49448089C>T
g.49054306C>T
510+1G>A, splice site
-
KMT2D_000528
-
PubMed: Miyake 2013
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+?/.
1
4i
c.511-1G>A
r.spl
p.?
-
pathogenic (dominant)
g.49447924C>T
g.49054141C>T
-
-
KMT2D_000720
-
PubMed: de Billy 2019
-
-
De novo
-
-
-
-
-
Emanuele Agolini
-?/.
1
-
c.554G>A
r.(?)
p.(Arg185His)
-
likely benign
g.49447880C>T
g.49054097C>T
KMT2D(NM_003482.3):c.554G>A (p.R185H)
-
KMT2D_000829
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
5
c.588del
r.(?)
p.(Cys197Alafs*11)
-
pathogenic
g.49447849del
g.49054066del
588del, (Cys197Alafs*11)
-
KMT2D_000527
-
PubMed: Makrythanasis 2013
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
+/.
1
5
c.589del
r.(?)
p.(Cys197Alafs*11)
-
pathogenic
g.49447845del
g.49054062del
589del, (Cys197Alafs*11)
-
KMT2D_000526
-
PubMed: Makrythanasis 2013
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
5
c.626C>T
r.(?)
p.(Thr209Ile)
-
VUS
g.49447808G>A
g.49054025G>A
-
-
KMT2D_000071
-
PubMed: Micale 2014
-
-
Unknown
?
-
-
-
-
B. Augello
?/.
1
-
c.658G>A
r.(?)
p.(Gly220Arg)
-
VUS
g.49447776C>T
g.49053993C>T
-
-
KMT2D_000724
-
Journal: Reynhout 2019
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
5
c.669T>G
r.(?)
p.(Tyr223*)
-
pathogenic
g.49447765A>C
g.49053982A>C
669T>G, Tyr223X
-
KMT2D_000525
-
PubMed: Micale 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
-
c.674-7C>A
r.(=)
p.(=)
-
VUS
g.49447431G>T
g.49053648G>T
KMT2D(NM_003482.3):c.674-7C>A
-
KMT2D_000860
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
-
c.696dup
r.(?)
p.(Glu233Ter)
-
pathogenic
g.49447402dup
g.49053619dup
KMT2D(NM_003482.3):c.696dupT (p.E233*)
-
KMT2D_000828
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
+/.
1
6
c.697G>T
r.(?)
p.(Glu233*)
-
pathogenic
g.49447401C>A
g.49053618C>A
697G>T, E233X
-
KMT2D_000524
-
PubMed: Banka 2012
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+/.
1
6
c.702del
r.(?)
p.(Pro235Glnfs*26)
-
pathogenic
g.49447399del
g.49053616del
702delG, P235QfsX26
-
KMT2D_000523
-
PubMed: Hannibal 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+/.
1
6
c.705del
r.(?)
p.(Glu237Serfs*24)
-
pathogenic
g.49447393del
g.49053610del
705delA, Pro235ProfsX26
-
KMT2D_000522
-
PubMed: Micale 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
-?/.
1
-
c.711G>A
r.(?)
p.(Glu237=)
-
likely benign
g.49447387C>T
g.49053604C>T
KMT2D(NM_003482.3):c.711G>A (p.E237=)
-
KMT2D_000888
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
6
c.721del
r.(?)
p.(Leu241Cysfs*20)
-
pathogenic
g.49447378del
g.49053595del
721del, (Leu241Cysfs*20)
-
KMT2D_000521
-
PubMed: Dentici 2015
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
+/.
2
6
c.741T>A
r.(?)
p.(Cys247*)
-
pathogenic (dominant), pathogenic
g.49447357A>T
g.49053574A>T
741T>A, Cys247X
-
KMT2D_000520
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
De novo, Germline
yes
-
-
-
-
Nina Bögershausen
,
Vincent Gatinois
+/.
2
6
c.751dup
r.(?)
p.(Tyr251Leufs*22)
-
pathogenic (dominant), pathogenic
g.49447347dup
g.49053564dup
751dupT, Tyr251LeufsX22
-
KMT2D_000519
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
Germline
yes, ?
-
-
-
-
Nina Bögershausen
,
Vincent Gatinois
-?/.
1
-
c.812C>G
r.(?)
p.(Pro271Arg)
ACMG
likely benign
g.49447286G>C
g.49053503G>C
-
-
KMT2D_000953
-
PubMed: Faundes 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
6i
c.839+2T>A
r.spl
p.?
-
pathogenic (dominant)
g.49447257A>T
g.49053474A>T
-
-
KMT2D_000571
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
De novo
-
-
-
-
-
Nina Bögershausen
?/.
1
6i
c.839+69G>A
r.(=)
p.(=)
-
VUS
g.49447190C>T
g.49053407C>T
-
-
KMT2D_000104
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
+/.
1
6i
c.840-1G>A
r.spl
p.?
-
pathogenic
g.49447105C>T
g.49053322C>T
840-1G>A,
-
KMT2D_000518
-
PubMed: Hannibal 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
7
c.859A>G
r.(?)
p.(Lys287Glu)
-
VUS
g.49447085T>C
g.49053302T>C
-
-
KMT2D_000103
PolyPhen-2 benign score 0.009
-
-
-
Germline
-
-
-
-
-
Andreas Laner
+/.
1
7
c.859_860insT
r.(?)
p.(Lys287Ilefs*6)
-
pathogenic
g.49447084_49447085insA
g.49053301_49053302insA
859_860insT, (Lys287Ilefs*6)
-
KMT2D_000517
-
PubMed: Makrythanasis 2013
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
-?/.
1
-
c.879G>A
r.(?)
p.(Thr293=)
-
likely benign
g.49447065C>T
g.49053282C>T
KMT2D(NM_003482.3):c.879G>A (p.T293=)
-
KMT2D_000827
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
7i
c.954+1G>T
r.spl
p.?
-
pathogenic
g.49446989C>A
g.49053206C>A
954+1G>T,
-
KMT2D_000516
-
PubMed: Li 2011
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
+/.
1
7i
c.955-1G>A
r.spl?
p.?
-
pathogenic
g.49446856C>T
g.49053073C>T
-
-
KMT2D_000102
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-?/., +/.
2
8
c.1010C>T
r.(?)
p.(Ser337Leu)
-
likely benign, pathogenic
g.49446800G>A
g.49053017G>A
KMT2D(NM_003482.3):c.1010C>T (p.S337L), 1010C>T, S337L
-
KMT2D_000515
VKGL data sharing initiative Nederland
PubMed: Banka 2012
-
-
CLASSIFICATION record, Germline
?
-
-
-
-
VKGL-NL_Rotterdam
,
Vincent Gatinois
+/.
1
8
c.1012G>T
r.(?)
p.(Glu338*)
-
pathogenic
g.49446798C>A
g.49053015C>A
1012G>T, (Glu338*)
-
KMT2D_000514
-
PubMed: Makrythanasis 2013
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+/.
1
8
c.1035_1036del
r.(?)
p.(Cys346Serfs*17)
-
pathogenic
g.49446780_49446781del
g.49052997_49052998del
1035_1036delCT, Leu345LeufsX18
-
KMT2D_000513
-
PubMed: Micale 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
-
c.1040A>G
r.(?)
p.(His347Arg)
-
VUS
g.49446770T>C
g.49052987T>C
KMT2D(NM_003482.3):c.1040A>G (p.H347R)
-
KMT2D_000826
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.1042C>T
r.(?)
p.(Arg348Cys)
-
VUS
g.49446768G>A
g.49052985G>A
KMT2D(NM_003482.3):c.1042C>T (p.R348C)
-
KMT2D_000697
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.1115T>A
r.(?)
p.(Phe372Tyr)
-
likely benign
g.49446490A>T
g.49052707A>T
KMT2D(NM_003482.3):c.1115T>A (p.(Phe372Tyr))
-
KMT2D_000696
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-?/.
1
-
c.1120C>A
r.(?)
p.(Pro374Thr)
-
likely benign
g.49446485G>T
g.49052702G>T
KMT2D(NM_003482.3):c.1120C>A (p.P374T)
-
KMT2D_000887
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
2
9
c.1142_1143insACCC
r.(?)
p.(Thr382Profs*3)
-
pathogenic, pathogenic (dominant)
g.49446465_49446466insTGGG
g.49052682_49052683insTGGG
1142_1143insACCC, Pro381HisfsX3
-
KMT2D_000512
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
Germline, De novo
yes
-
-
-
-
Vincent Gatinois
,
Nina Bögershausen
-?/.
1
-
c.1143C>T
r.(?)
p.(Pro381=)
-
likely benign
g.49446462G>A
-
KMT2D(NM_003482.3):c.1143C>T (p.P381=)
-
KMT2D_000910
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
-
c.1149C>T
r.(?)
p.(Asp383=)
-
likely benign
g.49446456G>A
g.49052673G>A
KMT2D(NM_003482.3):c.1149C>T (p.D383=)
-
KMT2D_000825
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.1155C>T
r.(?)
p.(Pro385=)
-
likely benign
g.49446450G>A
g.49052667G>A
KMT2D(NM_003482.3):c.1155C>T (p.P385=)
-
KMT2D_000886
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
9
c.1187C>G
r.(?)
p.(Pro396Arg)
-
pathogenic
g.49446418G>C
g.49052635G>C
1187C>G, Pro396Arg
-
KMT2D_000511
-
-
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
-
c.1190A>C
r.(?)
p.(Lys397Thr)
-
VUS
g.49446415T>G
g.49052632T>G
KMT2D(NM_003482.3):c.1190A>C (p.K397T)
-
KMT2D_000859
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+?/.
2
-
c.1258+5G>A
r.spl?
p.?
-
likely pathogenic
g.49446342C>T
g.49052559C>T
KMT2D(NM_003482.3):c.1258+5G>A
-
KMT2D_000695
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Nijmegen
,
VKGL-NL_VUmc
-?/.
1
-
c.1277T>C
r.(?)
p.(Leu426Pro)
ACMG
likely benign
g.49446189A>G
g.49052406A>G
-
-
KMT2D_000952
-
PubMed: Faundes 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
10
c.1300del
r.(?)
p.(Leu434*)
-
pathogenic
g.49446171del
g.49052388del
1300delC, Leu434*
-
KMT2D_000510
-
PubMed: Miyake 2013
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+/.
1
10
c.1301del
r.(?)
p.(Leu434Glnfs*496)
-
pathogenic
g.49446165del
g.49052382del
1301delT, Leu434GlnfsX496
-
KMT2D_000509
-
PubMed: Paulussen 2011
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
-?/.
1
-
c.1305C>T
r.(?)
p.(Asn435=)
-
likely benign
g.49446161G>A
g.49052378G>A
KMT2D(NM_003482.3):c.1305C>T (p.N435=)
-
KMT2D_000694
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
2
10
c.1328del
r.(?)
p.(Pro443Hisfs*487)
-
pathogenic
g.49446142del
g.49052359del
1328delC, Pro443Hisfs*487, 1324delC, P442HfsX487
-
KMT2D_000508
-
PubMed: Miyake 2013
,
PubMed: Ng 2010
,
PubMed: Hannibal 2011
-
-
Germline
yes, ?
-
-
-
-
Vincent Gatinois
+?/.
1
-
c.1329_1332del
r.(?)
p.(Pro444Argfs*485)
-
likely pathogenic
g.49446134_49446137del
g.49052351_49052354del
-
-
KMT2D_000871
11 heterozygous, no homozygous;
Clinindb (India)
PubMed: Narang 2020
,
Journal: Narang 2020
-
rs587783689
Germline
-
11/2622 individuals
-
-
-
Mohammed Faruq
+/.
2
10
c.1345_1346del
r.(?)
p.(Leu449Valfs*5)
-
pathogenic
g.49446120_49446121del
g.49052337_49052338del
1345_1346delCT, Leu449ValfsX5, 1345_1346del, (Leu449Valfs*5)
-
KMT2D_000507
-
PubMed: Micale 2011
,
PubMed: Dentici 2015
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+/.
2
10
c.1363del
r.(?)
p.(Glu455Asnfs*475)
-
pathogenic (dominant), pathogenic
g.49446104del
g.49052321del
1363delG, Glu455Asnfs*475
-
KMT2D_000506
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
Germline
yes, ?
-
-
-
-
Nina Bögershausen
,
Vincent Gatinois
?/.
1
10
c.1396C>T
r.(?)
p.(Arg466Cys)
ACMG
VUS
g.49446070G>A
g.49052287G>A
-
-
KMT2D_000967
-
PubMed: Squeo 2020
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
2
10
c.1425del
r.(?)
p.(Ala476Hisfs*454)
-
pathogenic (dominant), pathogenic
g.49446043del
g.49052260del
1425delC, Pro475ProfsX455
-
KMT2D_000505
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
De novo, Germline
yes
-
-
-
-
Nina Bögershausen
,
Vincent Gatinois
+/.
1
10
c.1448dup
r.(?)
p.(Leu483Phefs*17)
-
pathogenic
g.49446019dup
g.49052236dup
1446insT, L483FfsX17
-
KMT2D_000504
-
PubMed: Banka 2012
-
-
Germline
?
-
-
-
-
Vincent Gatinois
+/.
1
10
c.1483_1486del
r.(?)
p.(Ser495Argfs*434)
-
pathogenic
g.49445983_49445986del
g.49052200_49052203del
1483_1486delTCTC, S495RfsX434
-
KMT2D_000503
-
PubMed: Li 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
-
c.1487C>T
r.(?)
p.(Pro496Leu)
-
VUS
g.49445979G>A
g.49052196G>A
KMT2D(NM_003482.3):c.1487C>T (p.P496L)
-
KMT2D_000692
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
-?/.
1
-
c.1490C>T
r.(?)
p.(Pro497Leu)
ACMG
likely benign
g.49445976G>A
g.49052193G>A
-
-
KMT2D_000951
-
PubMed: Faundes 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
10
c.1503dup
r.(?)
p.(Pro502Serfs*7)
-
pathogenic
g.49445963dup
g.49052180dup
-
-
KMT2D_000003
-
PubMed: Micale 2014
-
-
De novo
-
-
-
-
-
Giuseppe Merla
+/.
1
10
c.1512_1513del
r.(?)
p.(Pro506Thrfs*2)
-
pathogenic
g.49445955_49445956del
g.49052172_49052173del
1512_1513delTC, P506TfsX2
-
KMT2D_000502
-
PubMed: Li 2011
-
-
Germline
yes
-
-
-
-
Vincent Gatinois
+/.
1
10
c.1530del
r.(?)
p.(Pro511Leufs*419)
-
pathogenic (dominant)
g.49445936del
g.49052153del
1530_1530delA
-
KMT2D_000721
-
PubMed: Martinez 2017
,
Journal: Martinez 2017
-
-
De novo
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.1568C>T
r.(?)
p.(Pro523Leu)
-
likely benign
g.49445898G>A
g.49052115G>A
KMT2D(NM_003482.3):c.1568C>T (p.P523L)
-
KMT2D_000885
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Utrecht
+/.
2
10
c.1576_1577del
r.(?)
p.(Ser526Thrfs*7)
-
pathogenic (dominant), pathogenic
g.49445889_49445890del
g.49052106_49052107del
1576_1577delTC, Ser526ThrfsX7
-
KMT2D_000501
-
PubMed: Bögershausen 2016
,
Journal: Bögershausen 2016
-
-
Germline
yes, ?
-
-
-
-
Nina Bögershausen
,
Vincent Gatinois
+/.
1
10
c.1628C>T
r.(?)
p.(Ser543Leu)
-
pathogenic
g.49445838G>A
g.49052055G>A
1628C>T, S543L
-
KMT2D_000500
-
PubMed: Li 2011
-
-
Germline
no
-
-
-
-
Vincent Gatinois
+/.
1
10
c.1634del
r.(?)
p.(Leu545Argfs*385)
-
pathogenic
g.49445832del
g.49052049del
1634delT, L545RfsX
-
KMT2D_000499
-
PubMed: Banka 2012
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
10
c.1660T>A
r.(?)
p.(Leu554Met)
-
VUS
g.49445806A>T
g.49052023A>T
-
-
KMT2D_000101
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
?/., +?/.
2
-
c.1667C>T
r.(?)
p.(Pro556Leu)
ACMG
VUS
g.49445799G>A
g.49052016G>A
-
-
KMT2D_000118
-
PubMed: Faundes 2018
,
PubMed: DDDS 2015
,
Journal: DDDS 2015
,
PubMed: Faundes 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
?/.
1
10
c.1668G>A
r.(=)
p.(=)
-
VUS
g.49445798C>T
g.49052015C>T
-
-
KMT2D_000100
-
-
-
-
Germline
-
-
-
-
-
Andreas Laner
-?/.
1
-
c.1725A>T
r.(?)
p.(Pro575=)
-
likely benign
g.49445741T>A
g.49051958T>A
KMT2D(NM_003482.3):c.1725A>T (p.P575=)
-
KMT2D_000823
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
?/.
1
-
c.1747C>G
r.(?)
p.(Pro583Ala)
ACMG
VUS
g.49445719G>C
g.49051936G>C
-
-
KMT2D_000950
-
PubMed: Faundes 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
-?/.
1
-
c.1762T>C
r.(?)
p.(Ser588Pro)
-
likely benign
g.49445704A>G
g.49051921A>G
KMT2D(NM_003482.3):c.1762T>C (p.S588P)
-
KMT2D_000691
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
+/.
1
10
c.1781C>T
r.(?)
p.(Pro594Leu)
-
pathogenic
g.49445685G>A
g.49051902G>A
1781C>T, Pro594Leu
-
KMT2D_000498
-
-
-
-
Germline
no
-
-
-
-
Vincent Gatinois
-?/.
1
-
c.1793G>A
r.(?)
p.(Arg598His)
-
likely benign
g.49445673C>T
g.49051890C>T
KMT2D(NM_003482.3):c.1793G>A (p.R598H)
-
KMT2D_000690
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
2
-
c.1797G>A
r.(?)
p.(Leu599=)
-
likely benign
g.49445669C>T
g.49051886C>T
KMT2D(NM_003482.3):c.1797G>A (p.L599=)
-
KMT2D_000858
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Rotterdam
,
VKGL-NL_AMC
-?/.
1
-
c.1850T>A
r.(?)
p.(Leu617His)
-
likely benign
g.49445616A>T
g.49051833A>T
KMT2D(NM_003482.3):c.1850T>A (p.L617H)
-
KMT2D_000689
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
-?/.
1
-
c.1888C>T
r.(?)
p.(Pro630Ser)
ACMG
likely benign
g.49445578G>A
g.49051795G>A
-
-
KMT2D_000949
-
PubMed: Faundes 2018
-
-
Germline
-
-
-
-
-
Johan den Dunnen
+/.
1
10
c.1914del
r.(?)
p.(Pro639Leufs* 291)
ACMG
pathogenic
g.49445552del
g.49051769del
-
-
KMT2D_000966
-
PubMed: Squeo 2020
-
-
Germline/De novo (untested)
-
-
-
-
-
Johan den Dunnen
+/.
1
10
c.1921G>T
r.(?)
p.(Glu641*)
-
pathogenic
g.49445545C>A
g.49051762C>A
1921G>T, Glu641X
-
KMT2D_000497
-
PubMed: Micale 2011
-
-
Germline
?
-
-
-
-
Vincent Gatinois
?/.
1
-
c.1923A>C
r.(?)
p.(Glu641Asp)
-
VUS
g.49445543T>G
g.49051760T>G
KMT2D(NM_003482.3):c.1923A>C (p.E641D)
-
KMT2D_000688
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Groningen
?/.
1
-
c.1930A>C
r.(?)
p.(Met644Leu)
-
VUS
g.49445536T>G
g.49051753T>G
KMT2D(NM_003482.3):c.1930A>C (p.(Met644Leu))
-
KMT2D_000687
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_Leiden
-/.
1
-
c.1938C>G
r.(?)
p.(Pro646=)
-
benign
g.49445528G>C
g.49051745G>C
KMT2D(NM_003482.3):c.1938C>G (p.P646=)
-
KMT2D_000884
VKGL data sharing initiative Nederland
-
-
-
CLASSIFICATION record
-
-
-
-
-
VKGL-NL_AMC
-?/., +/.
3
10, 14
c.1940C>A
r.(?)
p.(Pro647Gln)
-
likely benign, pathogenic
g.49445526G>T
g.49051743G>T
KMT2D(NM_003482.3):c.1940C>A (p.P647Q), 1940C>A, P647Q, 1940C>A, (Pro647Gln)
-
KMT2D_000496
VKGL data sharing initiative Nederland
PubMed: Li 2011
,
PubMed: Makrythanasis 2013
-
-
CLASSIFICATION record, Germline
?, yes
-
-
-
-
VKGL-NL_Utrecht
,
Vincent Gatinois
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