rs128624214
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000033.4(ABCD1):c.1451C>G(p.Pro484Arg) 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P484S) 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 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1451C>G | p.Pro484Arg | missense_variant | 5/10 | ENST00000218104.6 | |
LOC124905226 | XR_007068350.1 | n.3137G>C | non_coding_transcript_exon_variant | 2/2 | |||
ABCD1 | XM_047441916.1 | c.1751C>G | p.Pro584Arg | missense_variant | 6/11 | ||
ABCD1 | XM_047441917.1 | c.1507C>G | p.Pro503Ala | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.1451C>G | p.Pro484Arg | missense_variant | 5/10 | 1 | NM_000033.4 | P1 | |
PLXNB3-AS1 | ENST00000434284.1 | n.580+856G>C | intron_variant, non_coding_transcript_variant | 3 | |||||
ABCD1 | ENST00000443684.2 | n.454C>G | non_coding_transcript_exon_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 24
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 30, 1994 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at