| Literature DB >> 32274456 |
Justin Chun1,2, Minxian Wang1,3, Maris S Wilkins1, Andrea U Knob1, Ava Benjamin1, Lihong Bu4, Martin R Pollak1.
Abstract
INTRODUCTION: Focal segmental glomerulosclerosis (FSGS) is a histopathologically defined kidney lesion. FSGS can be observed with various underlying causes, including highly penetrant monogenic renal disease. We recently identified pathogenic variants of UMOD, a gene encoding the tubular protein uromodulin, in 8 families with suspected glomerular disease.Entities:
Keywords: ADTKD; FSGS; UMOD; UMOD-associated kidney disease; autosomal dominant tubulointerstitial kidney disease; chronic kidney disease; exome sequencing; glomerular disease; uromodulin
Year: 2020 PMID: 32274456 PMCID: PMC7136358 DOI: 10.1016/j.ekir.2019.12.016
Source DB: PubMed Journal: Kidney Int Rep ISSN: 2468-0249
Primer sequences for UMOD used in this study
| Family | Forward primer | Reverse primer |
|---|---|---|
| FGCM, FGCO, FGGR | TGCCCACCACATTGACACAT | TTCTGTCCACAGGATGGTGC |
| FGDC, FGJF | ACTCACAGTGCCATCCATCC | AACCCTGAAGCTGGGCTTTT |
| FGJD | AGCCTCTTGCCGGCTTTAAT | GAGTGTCACCTGGCGTACTG |
| FGIT | GGATGAGGACTGTGGGGAGA | GGATGGATGGCACTGTGAGT |
Figure 1Pedigrees for 8 families with uromodulin (UMOD) variants. Pedigrees for families FGCM, FGIT, FGCO, FGLV, FGGR, FGDC, FGJF, and FGJD. Affected individuals with impaired kidney function are indicated in filled circles (female) and squares (male), and unfilled circles and squares for family members not on renal replacement therapy, but with otherwise unknown or unaffected status. Individuals who had exome sequencing of samples are indicated with a red outline. Sanger sequencing showing wild-type (REF, reference alleles) sequence and mutation (ALT, alternative alleles) are highlighted in green and red, respectively.
Figure 2Uromodulin (UMOD) variants in 8 families. Chromatograms of unaffected wild-type (WT) and UMOD variants for representative affecteds for FGCM, FGCO, and FGGR (in-frame deletions), and FGDC, FGJF, FGJD, and FGIT (missense mutation; codon for mutation underlined). ALT, alternative; C, cysteine; F, phenylalanine; G, glycine; R, arginine; REF, reference; S, serine; W, tryptophan.
Rare variant list for the UMOD gene
| Family | POS_HG19 | REF | ALT | HGVSp | HGVSc |
|---|---|---|---|---|---|
| FGJD | 20359574 | C | A | ENSP00000306279.4: p.Cys315Phe | ENST00000302509.4: c.944G>T |
| FGIT | 20360018 | C | G | ENSP00000306279.4: p.Trp202Ser | ENST00000302509.4: c.605G>C |
| FGDC | 20360306 | C | A | ENSP00000306279.4: p.Cys106Phe | ENST00000302509.4: c.317G>T |
| FGCM | 20360333 | CCTTCGGGGCAGA | CAGGAGGCGG | ENSP00000306279.4: p.Val93_Gly97delinsAlaAlaSerCys | ENST00000302509.4: c.278_289delinsCCGCCTCCT |
| FGLV | 20361045 | G | C | ENSP00000460845.1: p.Arg79Gly | ENST00000574195.1: c.235C>G |
| G48055 (control) | 20348046 | AG | CA | ENSP00000306279.4: p.Cys582Gly | ENST00000302509.4: c.1743_1744delinsTG |
ALT, alternative nucleotide(s); HG19, human genome assembly from Genome Reference Consortium; HGVSc, the Human Genome Variation Society notation for coding sequence name; HGVSp, the Human Genome Variation Society notation for protein sequence name; POS, genomic position; REF, reference nucleotide(s).
Transcripts: Ensembl transcripts available at www.ensembl.org.
Figure 3Schematic representation for the relative locations of uromodulin (UMOD) variants. (a) UMOD transcript ENST00000302509.4 displaying exons 1 to 11 of with the locations of 4 mutations. The location of in-frame deletions and missense substitutions are indicated by single-letter amino acid codes. The mutations in the present study were found in exons 3 and 4. An open reading frame predicts a 640–amino acid protein for uromodulin. The protein domains of UMOD include 3 epidermal growth factor-like domains denoted by I, II, and III, cysteine-rich region containing the domain of 8 cysteines (D8C). The in-frame deletions and the missense mutations found in the present study are indicated. (b) UMOD transcript ENST00000574195.1 displaying exons 1 to 4 for family FGLV with the location of one newly identified mutation. The open reading frame encoded by exons 1 to 3 predicts a 161–amino acid protein for uromodulin. The predicted protein domains for this transcript include 2 epidermal growth factor-like domains denoted by I and II.
In silico prediction scores of clinical pathogenicity for UMOD variants
| Family | Nucleotide change | GnomAD_ genomes_AF | CLIN_SIG | PolyPhen-2 | SIFT | MetaSVM | M-CAP | LRT | GERP++_RS | CADD_ PHRED |
|---|---|---|---|---|---|---|---|---|---|---|
| FGJD | c.944G>T | 0 | NA | D | D | D | D | D | 4.64 | 32 |
| FGIT | c.605G>C | 0 | NA | D | D | D | D | D | 5.13 | 32 |
| FGDC | c.317G>T | 0 | Likely pathogenic | D | D | D | D | D | 5.45 | 28 |
| FGCM | c.278_289delins | 0 | Pathogenic | NA | NA | NA | NA | NA | NA | 20.4 |
| FGLV | c.235C>G | 0 | NA | NA | NA | NA | NA | NA | NA | 0.566 |
| G48055 (control) | c.1743_1744 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
CLIN_SIG, Clinvar database annotation signature; D, deleterious; GnomAD_genomes_AF, variant frequency in GnomAD database; NA, not applicable.
Prediction tools for predicting deleteriousness of single nucleotide variants or insertion/deletion variants: PolyPhen-2, Polymorphism Phenotyping v2; SIFT, Sorting Tolerant From Intolerant; M-CAP, Mendelian Clinically Applicable Pathogenicity; LRT, likelihood ratio test; GERP++RS, Genomic Evolutionary Rate Profiling rejected substitution; and CADD, Combined Annotation Dependent Depletion.
Phenotype information for 8 families with UMOD variants
| Family | Individual | Sex | Age at diagnosis | Age of ESRD | Hematuria | Proteinuria (ACR or mg/d) | SCr (mg/dl) | Working diagnosis | Biopsy findings c/w FSGS |
|---|---|---|---|---|---|---|---|---|---|
| FGCM | 111 | M | U | 58 | Neg | Pos (1100) | U | Hereditary GN | U |
| FGCM | 112 | M | 55 | 55 | Neg | Pos | U | ESRD NYD | U |
| FGCM | 113 | M | 25 | 40 | U | Pos | U | Hereditary GN | U |
| FGCM | 115 | F | 32 | 39 | Pos | Pos | 11.2 | ESRD NYD | U |
| FGCM | 117 | F | U | 50 | U | Pos (278) | 1.9 | Hereditary GN | Global and segmental sclerosis |
| FGCM | 118 | M | 34 | U | U | Pos | U | Hereditary GN | U |
| FGCM | 1141 | M | U | 57 | U | U | U | ESRD NYD | U |
| FGCM | 1151 | M | U | 36 | Neg | U | U | ESRD NYD | U |
| FGCO | 122 | F | 40 | 47 | U | U | U | ESRD from HTN | U |
| FGCO | 1111 | F | 41 | 42 | Neg | U | 1 | Hereditary GN | U |
| FGGR | 111 | M | 54 | 55 | Pos | Pos (130.7) | 1.6 | Hereditary GN | U |
| FGGR | 114 | M | 40 | 49 | Neg | Pos (84.5) | 1.5 | FSGS | FSGS |
| FGGR | 151 | M | 44 | 52 | Neg | Pos (>303) | 3.2 | FSGS | FSGS |
| FGGR | 152 | M | U | 50 | Neg | Pos (>629) | U | NS NYD | U |
| FGGR | 311 | M | 57 | N/A | Neg | U | 4 | Hereditary GN | U |
| FGDC | 111 | F | U | 45 | U | Pos | U | FSGS | FSGS |
| FGDC | 112 | F | 40 | 46 | Neg | Pos | 1.1 | FSGS | FSGS |
| FGIT | 1 | M | U | 45 | Neg | Neg | U | Hereditary GN | U |
| FGIT | 11 | F | 20 | 21 | Neg | Pos (175 mg/d) | 1.6 | Hereditary TIN | Effaced FPs |
| FGIT | 12 | M | 38 | N/A | Neg | Pos (165.5) | 2.4 | CKD NYD | None |
| FGIT | 21 | F | 37 | 68 | Neg | Pos (72) | 1.4 | Hereditary GN | U |
| FGIT | 22 | M | 36 | 45 | Neg | Neg | 1 | Hereditary GN | U |
| FGIT | 234 | F | 29 | 35 | U | Neg | 3.2 | HTN related | None |
| FGJD | 1 | F | U | 69 | U | U | U | HTN related | U |
| FGJD | 11 | M | 16 | 36 | Neg | Neg | 7.9 | FSGS | FSGS |
| FGJF | 3 | F | U | 40 | Neg | Neg | 1.9 | FSGS | U |
| FGJF | 11 | F | U | 51 | Neg | Neg | 1.7 | FSGS | FSGS |
| FGJF | 13 | F | U | 40 | Neg | Neg | U | FSGS | None |
| FGJF | 32 | F | 34 | 36 | Neg | Pos (700 mg/d) | 2.5 | FSGS | FSGS |
| FGLV | 115 | F | U | 60 | Pos | Pos (298.8) | 3.5 | Hereditary GN | U |
| FGLV | 116 | F | U | 51 | Neg | Neg | 1.9 | ESRD NYD | U |
| FGLV | 1121 | M | 47 | 52 | Neg | Pos | U | ESRD NYD | U |
| FGLV | 1133 | M | 37 | 42 | Pos | Neg | 2.4 | ESRD NYD | U |
| FGLV | 1153 | F | U | 40 | Neg | Pos (30.9) | 1.2 | ESRD NYD | U |
ACR, albumin-to-creatinine ratio in mg/g; CKD, chronic kidney disease; c/w, consistent with; ESRD, end-stage renal disease; F, female; FPs, foot processes; FSGS, focal segmental glomerulosclerosis; GN, glomerulonephritis; IgAN, IgA nephropathy; M, male; Neg, negative; none, no findings consistent with FSGS; NS, nephrotic syndrome; NYD, not yet determined; Pos, positive; SCr, serum creatinine; TIN, tubulointerstitial nephritis; U, unknown.
Insufficient material for native kidneys; based on biopsies of 2 allografts showing FSGS (suspected FSGS recurrence).
Figure 4Family FGJF proband (FGJF32) biopsy showing focal segmental glomerulosclerosis (FSGS). Glomerulus stained with (a) periodic acid–Schiff and (b) hematoxylin and eosin showing focal segmental sclerosis. Localized podocyte foot process changes. Extensive tubular atrophy and interstitial fibrosis were present in other regions (not shown here). Bar = 30 μm. (c) Electron microscopy from FGJF32 showing segments of glomerular tufts with segmental collapse and sclerosis of capillary loops. Segmental fusion of foot processes and microvillous transformation of visceral epithelial cells. No evidence of immune complex deposition or inflammation or cell proliferation. Bar = 1 μm.