19-35718056-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014727.3(KMT2B):​c.38C>T​(p.Pro13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000405 in 986,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000036 ( 0 hom. )

Consequence

KMT2B
NM_014727.3 missense

Scores

2
1
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.266
Variant links:
Genes affected
KMT2B (HGNC:15840): (lysine methyltransferase 2B) This gene encodes a protein which contains multiple domains including a CXXC zinc finger, three PHD zinc fingers, two FY-rich domains, and a SET (suppressor of variegation, enhancer of zeste, and trithorax) domain. The SET domain is a conserved C-terminal domain that characterizes proteins of the MLL (mixed-lineage leukemia) family. This gene is ubiquitously expressed in adult tissues. It is also amplified in solid tumor cell lines, and may be involved in human cancer. Two alternatively spliced transcript variants encoding distinct isoforms have been reported for this gene, however, the full length nature of the shorter transcript is not known. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13873413).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KMT2BNM_014727.3 linkc.38C>T p.Pro13Leu missense_variant 1/37 ENST00000420124.4 NP_055542.1 Q9UMN6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KMT2BENST00000420124.4 linkc.38C>T p.Pro13Leu missense_variant 1/371 NM_014727.3 ENSP00000398837.2 Q9UMN6
KMT2BENST00000673918.2 linkc.38C>T p.Pro13Leu missense_variant 1/37 ENSP00000501283.1 A0A669KBI7
KMT2BENST00000687718.1 linkn.38C>T non_coding_transcript_exon_variant 1/3 ENSP00000510535.1 A0A8I5KWP7
KMT2BENST00000692961.1 linkn.38C>T non_coding_transcript_exon_variant 1/36 ENSP00000509289.1 A0A8I5KPK0

Frequencies

GnomAD3 genomes
AF:
0.00000682
AC:
1
AN:
146606
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000494
GnomAD4 exome
AF:
0.00000357
AC:
3
AN:
840212
Hom.:
0
Cov.:
31
AF XY:
0.00000772
AC XY:
3
AN XY:
388820
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000261
Gnomad4 OTH exome
AF:
0.0000361
GnomAD4 genome
AF:
0.00000682
AC:
1
AN:
146606
Hom.:
0
Cov.:
32
AF XY:
0.0000140
AC XY:
1
AN XY:
71338
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000494
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Dystonia 28, childhood-onset Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingDepartment of Human Genetics, Hannover Medical SchoolJan 17, 2025ACMG: PM2_Supporting, BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Benign
-0.10
T
BayesDel_noAF
Benign
-0.38
CADD
Benign
23
DANN
Benign
0.91
DEOGEN2
Benign
0.027
T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.073
N
LIST_S2
Benign
0.54
T
M_CAP
Pathogenic
0.95
D
MetaRNN
Benign
0.14
T
MetaSVM
Benign
-0.85
T
MutationAssessor
Benign
0.0
N
PrimateAI
Pathogenic
0.89
D
PROVEAN
Benign
-0.50
N
REVEL
Benign
0.23
Sift
Benign
0.68
T
Sift4G
Benign
0.17
T
Polyphen
0.0
B
Vest4
0.15
MutPred
0.20
Gain of catalytic residue at P13 (P = 0.0193);
MVP
0.20
ClinPred
0.022
T
GERP RS
-0.44
Varity_R
0.064
gMVP
0.20

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1969021720; hg19: chr19-36208958; API