rs797044610
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PS1PM1PM2PM5PP3_StrongPP5_Moderate
The NM_000033.4(ABCD1):c.887A>C(p.Tyr296Ser) 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 Likely pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y296C) 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 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.887A>C | p.Tyr296Ser | missense_variant | 1/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.887A>C | p.Tyr296Ser | missense_variant | 1/11 | ||
ABCD1 | XM_047441917.1 | c.887A>C | p.Tyr296Ser | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.887A>C | p.Tyr296Ser | missense_variant | 1/10 | 1 | NM_000033.4 | P1 | |
ABCD1 | ENST00000370129.4 | c.332A>C | p.Tyr111Ser | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 26
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 26
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 23, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at