chr11-74342508-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_173582.6(PGM2L1):c.1585C>T(p.Arg529Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000025 in 1,602,584 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. R529Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_173582.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM2L1 | NM_173582.6 | c.1585C>T | p.Arg529Trp | missense_variant | 12/14 | ENST00000298198.5 | |
LOC112268078 | XR_002957258.2 | n.314+13020G>A | intron_variant, non_coding_transcript_variant | ||||
PGM2L1 | XM_011544953.4 | c.1648C>T | p.Arg550Trp | missense_variant | 13/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM2L1 | ENST00000298198.5 | c.1585C>T | p.Arg529Trp | missense_variant | 12/14 | 1 | NM_173582.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151890Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000327 AC: 8AN: 244372Hom.: 0 AF XY: 0.0000227 AC XY: 3AN XY: 132130
GnomAD4 exome AF: 0.0000248 AC: 36AN: 1450694Hom.: 0 Cov.: 32 AF XY: 0.0000153 AC XY: 11AN XY: 721134
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151890Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74166
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2023 | The c.1585C>T (p.R529W) alteration is located in exon 12 (coding exon 12) of the PGM2L1 gene. This alteration results from a C to T substitution at nucleotide position 1585, causing the arginine (R) at amino acid position 529 to be replaced by a tryptophan (W). 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