chr16-72017043-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001361.5(DHODH):c.454G>A(p.Gly152Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,613,816 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 (★★).
Frequency
Consequence
NM_001361.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHODH | NM_001361.5 | c.454G>A | p.Gly152Arg | missense_variant | Exon 4 of 9 | ENST00000219240.9 | NP_001352.2 | |
DHODH | XM_047433674.1 | c.370G>A | p.Gly124Arg | missense_variant | Exon 4 of 9 | XP_047289630.1 | ||
DHODH | XM_005255829.5 | c.25G>A | p.Gly9Arg | missense_variant | Exon 2 of 7 | XP_005255886.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000761 AC: 19AN: 249544Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135400
GnomAD4 exome AF: 0.000151 AC: 221AN: 1461798Hom.: 0 Cov.: 32 AF XY: 0.000142 AC XY: 103AN XY: 727206
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74252
ClinVar
Submissions by phenotype
Miller syndrome Pathogenic:1Uncertain:1
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The DHODH c.454G>A (p.Gly152Arg) variant is a missense variant that has been identified in a compound heterozygous state in two siblings with Miller syndrome, another name for postaxial acrofacial dysostosis (Ng et al. 2010; Roach et al. 2010). This variant was not identified in 237 control individuals but is reported at a frequency of 0.000180 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies performed by Fang et al. (2012) suggested the p.Gly152Arg variant affects protein expression or turnover. In addition, Rainger et al. (2012) determined that the variant enzyme shows reduced activity compared to wild type, although a larger effect was observed using a complementation assay than an in vitro assay of enzyme activity. The evidence for this variant is limited. The p.Gly152Arg variant is thus classified as of a variant of unknown significance but suspicious for pathogenicity for postaxial acrofacial dysostosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
not provided Uncertain:1
This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 152 of the DHODH protein (p.Gly152Arg). This variant is present in population databases (rs267606766, gnomAD 0.01%). This missense change has been observed in individual(s) with Miller syndrome (PMID: 19915526, 20220176). It has also been observed to segregate with disease in related individuals. This variant is also known as chr16:70608443 G>R. ClinVar contains an entry for this variant (Variation ID: 16803). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects DHODH function (PMID: 22692683, 22967083). 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