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Table 1 Summary of genetic variants identified in the patient by genome-wide scan

From: SCP2 variant is associated with alterations in lipid metabolism, brainstem neurodegeneration, and testicular defects

Disease (Inheritance)

Gene (Transcript)

Variant; Zygosity

Variant interpretation

Variant frequency (GnomAD)

Osteosclerotic metaphyseal dysplasia (AR); Parkinson’s disease (preliminary evidence, inheritance unknown)

LRRK1 (NM_024652.6)

c.4909A > T; Heterozygous

Variant of uncertain significance

0

Beta-mannosidosis (AR)

MANBA (NM_005908.3)

c.1622G > A; Heterozygous

Likely pathogenic

0.000008

Leukoencephalopathy with dystonia and motor neuropathy (AR)

SCP2 (NM_002979.5)

c.572A > G; Heterozygous

Variant of uncertain significance

0.00004

Dent disease (XLR); Hypophosphatemic rickets (XLR); Nephrolithiasis, type I (XLR); Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis (XLR)

CLCN5 (NM_001127898.4)

c.152G > A, Heterozygous

Variant of uncertain significance

0.00001265 total; 0.00001685 in females;

0 in males

Hypokalemic periodic paralysis, type 1 (AD); Susceptibility to malignant hyperthermia (AD); Susceptibility to thyrotoxic periodic paralysis (AD)

CACNA1S (NM_000069.3)

c.262A > G, Heterozygous

Variant of uncertain significance

0.0002369

  1. AR Autosomal recessive; AD autosomal dominant; XLR X-linked recessive