rs17856033
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024079.5(ALG8):βc.1507A>Gβ(p.Ile503Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000815 in 1,614,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (β β ).
Frequency
Consequence
NM_024079.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG8 | NM_024079.5 | c.1507A>G | p.Ile503Val | missense_variant | 13/13 | ENST00000299626.10 | NP_076984.2 | |
ALG8 | XM_005274247.4 | c.1480A>G | p.Ile494Val | missense_variant | 13/13 | XP_005274304.1 | ||
ALG8 | NM_001007027.3 | c.*178A>G | 3_prime_UTR_variant | 14/14 | NP_001007028.1 | |||
ALG8 | XR_950044.4 | n.1405A>G | non_coding_transcript_exon_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALG8 | ENST00000299626.10 | c.1507A>G | p.Ile503Val | missense_variant | 13/13 | 1 | NM_024079.5 | ENSP00000299626.5 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000493 AC: 124AN: 251366Hom.: 0 AF XY: 0.000574 AC XY: 78AN XY: 135830
GnomAD4 exome AF: 0.000860 AC: 1257AN: 1461886Hom.: 0 Cov.: 33 AF XY: 0.000850 AC XY: 618AN XY: 727248
GnomAD4 genome AF: 0.000387 AC: 59AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74496
ClinVar
Submissions by phenotype
Polycystic liver disease 3 with or without kidney cysts Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Immunogenetics and Transplant Biology Service, University Hospital "CittΓ della Salute e della Scienza di Torino" | Jul 03, 2023 | - - |
ALG8 congenital disorder of glycosylation;C4693472:Polycystic liver disease 3 with or without kidney cysts Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 23, 2015 | - - |
ALG8-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 28, 2024 | The ALG8 c.1507A>G variant is predicted to result in the amino acid substitution p.Ile503Val. This variant has been reported in a father with renal cysts and liver microcysts and his pediatric daughter with renal cysts (Saglia et al. 2023. PubMed ID: 38012624). However, this variant has also been reported in 0.14% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Of note, the p.Ile503 residue is not well conserved during evolution and at this position is a valine (Val) in multiple species including chimp. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
ALG8 congenital disorder of glycosylation Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 503 of the ALG8 protein (p.Ile503Val). This variant is present in population databases (rs17856033, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with ALG8-related conditions. ClinVar contains an entry for this variant (Variation ID: 284641). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ALG8 protein function with a negative predictive value of 80%. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at