16-16190294-T-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_001171.6(ABCC6):c.1505A>T(p.Lys502Met) 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 Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K502R) has been classified as Pathogenic.
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.1505A>T | p.Lys502Met | missense_variant | 12/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.1163A>T | p.Lys388Met | missense_variant | 12/31 | ||
ABCC6 | NR_147784.1 | n.1542A>T | non_coding_transcript_exon_variant | 12/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.1505A>T | p.Lys502Met | missense_variant | 12/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000622290.5 | c.1505A>T | p.Lys502Met | missense_variant, NMD_transcript_variant | 12/32 | 5 | |||
ABCC6 | ENST00000456970.6 | c.1505A>T | p.Lys502Met | missense_variant, NMD_transcript_variant | 12/29 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 35
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:1
Uncertain significance, no assertion criteria provided | research | PXE International | Feb 16, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at