NM_001085382.2:c.1403C>A
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001085382.2(PSAPL1):c.1403C>A(p.Ala468Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000019 in 1,579,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A468V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001085382.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSAPL1 | ENST00000319098.7 | c.1403C>A | p.Ala468Asp | missense_variant | Exon 1 of 1 | 6 | NM_001085382.2 | ENSP00000317445.4 | ||
SORCS2 | ENST00000507866.6 | c.548+37122G>T | intron_variant | Intron 2 of 26 | 1 | NM_020777.3 | ENSP00000422185.2 | |||
SORCS2 | ENST00000511199.1 | n.163+37122G>T | intron_variant | Intron 2 of 5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00000481 AC: 1AN: 207946 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1427012Hom.: 0 Cov.: 63 AF XY: 0.00000142 AC XY: 1AN XY: 706338 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74352 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1403C>A (p.A468D) alteration is located in exon 1 (coding exon 1) of the PSAPL1 gene. This alteration results from a C to A substitution at nucleotide position 1403, causing the alanine (A) at amino acid position 468 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at