NM_003482.4:c.3392C>G
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_003482.4(KMT2D):c.3392C>G(p.Pro1131Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1131L) has been classified as Likely benign.
Frequency
Consequence
NM_003482.4 missense
Scores
Clinical Significance
Conservation
Publications
- choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndromeInheritance: AD Classification: DEFINITIVE, MODERATE Submitted by: Illumina, G2P
- Kabuki syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Laboratory for Molecular Medicine, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
- branchial arch abnormalities, choanal atresia, athelia, hearing loss, and hypothyroidism syndromeInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Kabuki syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KMT2D | ENST00000301067.12 | c.3392C>G | p.Pro1131Arg | missense_variant | Exon 12 of 55 | 5 | NM_003482.4 | ENSP00000301067.7 | ||
KMT2D | ENST00000683543.2 | c.3392C>G | p.Pro1131Arg | missense_variant | Exon 12 of 56 | ENSP00000506726.1 | ||||
KMT2D | ENST00000685166.1 | c.3392C>G | p.Pro1131Arg | missense_variant | Exon 11 of 54 | ENSP00000509386.1 | ||||
KMT2D | ENST00000692637.1 | c.3392C>G | p.Pro1131Arg | missense_variant | Exon 11 of 54 | ENSP00000509666.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000121 AC: 3AN: 247644 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461500Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727050 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Kabuki syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at