Skip to main content

Table 1 Examples of disease-causing variation with associated HGVS nomenclature

From: Genome annotation for clinical genomic diagnostics: strengths and weaknesses

Location Gene Variation HGVS nomenclature ACMG clinical significance Associated disorder Reference
5′ UTR FMR1 Expansion NM_002024.5(FMR1):c.-128_-126(200) Pathogenic Fragile X syndrome [186]
CDS GRIN2A Nonsense NM_000833.4(GRIN2A):c.2041C > T (p.Arg681Ter) Pathogenic Idiopathic focal epilepsy (IFE) with rolandic spikes is the most common childhood epilepsy [187]
CDS GABRB3 Missense NM_021912.4(GABRB3):c.745C > A (p.Gln249Lys) Pathogenic Early infantile epileptic encephalopathy (EIEE) [188]
CDS WDR62 Deletion/frameshift NM_001083961.1(WDR62):c.3839_3855del17 (p.Gly1280Alafs) Pathogenic Malformations of cortical development [189]
3′ UTR MECP2 SNV NM_004992.3(MECP2):c.*2956G > A Uncertain significance Rett syndrome [190]
Promoter CRH SNV NC_000008.11:g.66178947G > T Pathogenic Familial autosomal dominant nocturnal frontal lobe epilepsy [191]
Splice site ATP6AP2 SNV NM_005765.2(ATP6AP2):c.321C > T (p.Asp107=) Pathogenic X-linked mental retardation and epilepsy due to inefficient inclusion of exon 4 [192]
Poly(A) ARSA SNV NM_000487.5(ARSA):c.*96A > G Pathogenic Metachromatic leukodystrophy [193]
NMD SNRPB SNV NM_003091.3(SNRPB):c.-72C > A Pathogenic Cerebro-costo-mandibular syndrome [194]
lncRNA ATXN8OS Insertion NR_002717.2(ATXN8OS):n.1103_1105CTG(15_40) Pathogenic Spinocerebellar ataxia type 8 [195]
  1. ACMG American College of Medical Genetics and Genomics, CDS coding sequence, HGVS Human Genome Variation Society, lncRNA long non-coding RNA, NMD nonsense-mediated decay, SNV single-nucleotide variant, UTR untranslated region