rs150976885
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_013339.4(ALG6):c.1135C>T(p.Pro379Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000428 in 1,612,942 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 (★★). Synonymous variant affecting the same amino acid position (i.e. P379P) has been classified as Likely benign.
Frequency
Consequence
NM_013339.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG6 | NM_013339.4 | c.1135C>T | p.Pro379Ser | missense_variant | 14/15 | ENST00000263440.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG6 | ENST00000263440.6 | c.1135C>T | p.Pro379Ser | missense_variant | 14/15 | 5 | NM_013339.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000459 AC: 67AN: 1460824Hom.: 0 Cov.: 31 AF XY: 0.0000482 AC XY: 35AN XY: 726706
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Submissions by phenotype
ALG6-congenital disorder of glycosylation 1C Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2022 | This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 379 of the ALG6 protein (p.Pro379Ser). This variant is present in population databases (rs150976885, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with ALG6-related conditions. ClinVar contains an entry for this variant (Variation ID: 128350). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | May 23, 2017 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 20, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at