rs864309715
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP2PP3_ModeratePP5_Moderate
The NM_001009999.3(KDM1A):c.1207G>A(p.Glu403Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E403A) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001009999.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM1A | NM_001009999.3 | c.1207G>A | p.Glu403Lys | missense_variant | 11/21 | ENST00000400181.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM1A | ENST00000400181.9 | c.1207G>A | p.Glu403Lys | missense_variant | 11/21 | 1 | NM_001009999.3 | ||
ENST00000427154.1 | n.261+19232C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 10, 2015 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | University of Washington Center for Mendelian Genomics, University of Washington | Sep 30, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at