Table 3.
Germline CDKN1B variants of interest in Cushing’s disease patients: evaluation of pathogenicity likelihood
| HGVSa nomenclature: DNA, protein | Location in gene, variant type | dbSNP ID | MAF in gnomAD (%) | Summary of in silico predictions | VarSomeb ACMG classification | Functional data | Clinical associations |
|---|---|---|---|---|---|---|---|
| c.-29_-26delAGAG, p.? | 5′ UTR, intronic. | rs774454456 | Exomes: 0.0376. Genomes: 0.0319. Exomes + genomes: 0.0369. | Mutation taster: disease causing; known disease mutation, protein features might be affected, splice site changes. Alamut: 5′ UTR substitution, the consequence of this change is not predictable, splice changes are unlikely. | Likely benign. | Previously reported c.- 32_-29delGAGA (6) is an equivalent deletion. Predicted altered 5′ UTR secondary structure; reduced mRNA levels and 5′ UTR transcriptional activity in vitro (6,9,32). Disrupts a GRE (9). Cytoplasmic localization by IHC in somatotropinoma (9) and negative staining in parathyroid adenoma (32). LOH in somatotropinoma (9). | Germline variant in one patient with gigantism (9), in one adult patient with gastric carcinoid tumor and PHPT (6), and in one patient with PHPT with a co-existent somatic homozygous frameshift MEN1 variant (32). HGMD (CD119870): disease causing. ClinVar (RCV000354456.1, RCV000210358.1, and RCV000162206.4): conflicting interpretation (likely benign, pathogenic, VUS). |
| c.320delA, p.Q107Rfs*12 | Exon 1, frameshift. | rs755301027 | Exomes: 0.0004. Genomes: n/a. | Mutation taster: disease causing; NMD, aa sequence changed, frameshift, protein features might be affected. Alamut: creates a frame shift starting at Q107; the new reading frame ends in a Stop codon 12 positions downstream. | Likely pathogenic. | n/a | n/a |
| c.356T>C, p.I119T | Exon 1, missense. | rs142833529 | Exomes: 0.0533. Genomes: 0.0637. Exomes + genomes: 0.0545. | Mutation taster: polymorphism; aa sequence changed, known disease mutation. SIFT: tolerated. PolyPhen 2: benign. Provean: neutral. Alamut: weakly conserved nucleotide, moderately conserved aa, moderate physicochemical difference between I and T (Grantham score: 89).c | Likely benign. | Nuclear localization, abnormal migration pattern (19,38), and increased protein stability (19). Loss of interaction with CDK6, but unaltered interaction with CDK1, CDK2, and CDK5 by pulldown assay (38). | Germline variant in the following cases: – One FIPA patient with acromegaly (19). – A 63-year-old woman with unclassified myeloproliferative syndrome (34). – One case of multiple myeloma (37). – One case of premature ovarian failure (36). – A family including 4 siblings with prostate cancer, a sister with lung cancer, and 4 unaffected carriers (33). – One patient from a cohort of secondary and tertiary hyperparathyroidism (35). – Present in a human renal cancer cell line (38). HGMD (CM054649): disease causing. ClinVar (RCV000563714.1, RCV000457158.3, and RCV000344750.1): conflicting interpretation (VUS, likely benign). |
| c.376G>C, p.E126Q | Exon 1, missense. | n/a. | Not found. | Mutation taster: polymorphism; aa sequence changed, protein features might be affected, splice site changes. SIFT: damaging. PolyPhen 2: probably damaging. Provean: neutral. Alamut: moderately conserved nucleotide, highly conserved aa, small physicochemical difference between E and Q (Grantham score: 29).c | VUS | n/a | None reported. Two variants have been described at this position: p.E126D, in a patient with PHPT (48), and p.E126K in a mouth squamous cell carcinoma sample in COSMIC (COSM5970591); somatic status not confirmed (54). |
| c.407A>G, p.D136G | Exon 1, missense. | rs546234840 | Exomes: 0.0069. Genomes: 0.0127. Exomes + genomes: 0.0075. | Mutation taster: disease causing; aa sequence changed, protein features might be affected, splice site changes. SIFT: damaging. PolyPhen 2: benign. Provean: neutral. Alamut: weakly conserved nucleotide, highly conserved aa, moderate physicochemical difference between D and G (Grantham score: 94).c | Likely benign. | n/a | COSMIC (COSM2227662): found in one head/ neck squamous cell carcinoma; somatic status not confirmed (55). ClinVar (RCV000475865.5 and RCV000346316.1): conflicting interpretation (VUS, likely benign). |
aa, amino acid; ACMG, American College of Medical Genetics and Genomics; FIPA, familial isolated pituitary adenoma; GRE, glucocorticoid-response element; MAF, minor allele frequency; MEN, multiple endocrine neoplasia; n/a, not available; NMD, nonsense-mediated mRNA decay; PHPT, primary hyperparathyroidism; UTR, untranslated region; VUS, variant of uncertain significance.
aAll variants were annotated according to the reference sequences NCBI GenBank NM_004064.4 and UniProt P46527-1.
bVarSome employs the Saphetor molecular database, which includes multiple databases for in silico prediction, frequency, disease associations and input from users.
cThe Grantham score calculates the evolutionary distance between two amino acids and ranges from 0 to 215. A larger score represents larger differences between two amino acids in terms of composition, polarity and molecular volume.