rs193922098
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_000033.4(ABCD1):c.838C>A(p.Arg280Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000882 in 113,411 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R280H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000033.4 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 |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.838C>A | p.Arg280Ser | missense_variant | 1/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.838C>A | p.Arg280Ser | missense_variant | 1/11 | ||
ABCD1 | XM_047441917.1 | c.838C>A | p.Arg280Ser | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.838C>A | p.Arg280Ser | missense_variant | 1/10 | 1 | NM_000033.4 | P1 | |
ABCD1 | ENST00000370129.4 | c.283C>A | p.Arg95Ser | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000882 AC: 1AN: 113357Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35499
GnomAD3 exomes AF: 0.00000776 AC: 1AN: 128935Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 33885
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1067640Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 342512
GnomAD4 genome AF: 0.00000882 AC: 1AN: 113411Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35563
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at