rs142925706
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 6P and 4B. PM1PM2PM5BP4_Strong
The ENST00000444124.7(DDC):c.178G>A(p.Val60Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,614,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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. V60A) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000444124.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDC | NM_001082971.2 | c.178G>A | p.Val60Ile | missense_variant | 2/15 | ENST00000444124.7 | NP_001076440.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDC | ENST00000444124.7 | c.178G>A | p.Val60Ile | missense_variant | 2/15 | 1 | NM_001082971.2 | ENSP00000403644 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251354Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135866
GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727236
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74474
ClinVar
Submissions by phenotype
Deficiency of aromatic-L-amino-acid decarboxylase Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 05, 2022 | This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 60 of the DDC protein (p.Val60Ile). This variant is present in population databases (rs142925706, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with DDC-related conditions. ClinVar contains an entry for this variant (Variation ID: 575126). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant disrupts the p.Val60 amino acid residue in DDC. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 28856607, 31953134, 31975548). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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