Background

LAMA5 biallelic gene variants causing congenital nephrotic syndrome (CNS) are rare entities and have recently been identified [1, 2]. Herein, we report a case of CNS with diffuse mesangial sclerosis (DMS) in a child of Indian origin due to compound heterozygous variants in the LAMA5 gene.

Case report

A two-and-a-half-month-old female infant presented with generalized edema for 10 days. She was born to non-consanguineous south Indian parents at term gestation with a birth weight of 2.2 kg, length 51 cm, and head circumference 35.5 cm. There was no history of fever with rash or drug intake in the antenatal period. Antenatal anomaly scans were normal with no evidence of oligohydramnios (amniotic fluid index being 13 cm at 37 weeks), intrauterine growth retardation or fetal cardiac abnormalities. There were no similar complaints in the family, and there was no history of miscarriage or fetal death in the past.

At presentation, she had periorbital puffiness, moderate ascites, and pedal edema. She was hemodynamically stable with blood pressure 82/38 mmHg (50–90th centile). The weight 4.5 kg (0.88 z), length 60 cm (1.28 z), and head circumference 39.5 cm (0.43 z) were normal. There were no features such as absent patella, hypoplastic nails, microcoria, lens abnormalities, or hypotonia. She had normal female genitalia, with no ambiguity. There was no hepatosplenomegaly. The kidney and bladder were not palpable, and no genital edema was noted.

Laboratory investigations revealed serum albumin 1.3 g/dL, spot urine protein:creatinine ratio (Up:Uc) 20.87 mg/mg, total cholesterol 380 mg/dL, and serum creatinine 0.31 mg/dL. Urinalysis showed no red blood cells (RBCs) or casts. Kidney ultrasound showed mildly enlarged kidneys (right kidney length 5.4 cm (+ 2.71z), left kidney length 5.1 cm (+ 2.43 z)) with normal echogenicity, preserved corticomedullary differentiation, with no hydronephrosis. Urinary bladder was normal, and the baby had normal female reproductive organs. Serologies for human immunodeficiency virus (HIV), hepatitis B (HBV), hepatitis C (HCV), venereal disease research laboratory test (VDRL) for syphilis, cytomegalovirus (CMV) IgM and IgG, rubella IgM, and toxoplasma IgM by ELISA were negative. Karyotype was that of a normal female (46XX). She was diagnosed with CNS. Supportive care with regular albumin infusions, enalapril, and thyroxine supplementation was continued. However, edema was unremitting along with worsening oliguria, a maximum creatinine of 1.5 mg/dL during the clinical course and electrolyte abnormalities refractory to medical management, leading to suspicion of diffuse mesangial sclerosis (DMS). The parents did not opt for kidney replacement therapy, and the child eventually expired at 6 months of age.

Postmortem kidney biopsy revealed an increase in the mesangial matrix (without an increase in cellularity) and thickened glomerular basement membrane leading to obliteration of the capillary lumen and crowding of the podocytes, consistent with DMS (Fig. 1). Exome sequencing covering around 8500 clinically relevant genes revealed compound heterozygous variants in LAMA5 gene (NM_005560.6). Deoxyribonucleic acid (DNA) extracted from blood was used to perform targeted gene capture using a custom capture kit. The libraries were sequenced to mean depth of > 80–100 × on Illumina sequencing platform. Genome analysis toolkit (GATK) best practices framework for identification of germline variants in the sample using Sentieon was followed. The sequences obtained were aligned to human reference genome (Genome reference consortium Human build 38) using Burrows-Wheeler alignment algorithm. Sentieon haplotype caller was then used to identify variants in the sample. Clinically relevant variants in both coding and non-coding regions were annotated using published variants in the literature and a set of disease databases. Common variants were filtered, and non-synonymous variants effect was calculated using multiple algorithms such as Polymorphism Phenotyping v2 (PolyPhen-2), Sorting intolerant from tolerant (SIFT), MutationTaster2, and Likelihood ratio test (LRT). Clinically significant variants were reported. There was a heterozygous likely pathogenic variant in exon 2: LAMA5: c.385C > A (depth 195 ×) that resulted in the amino acid substitution of lysine for glutamine at codon 129 (p.Gln129Lys) and another heterozygous pathogenic variant in exon 31: LAMA5: c.3932_3936dup (depth 174 ×) resulting in frameshift and premature truncation of the protein 44 amino acids downstream to codon 1313 (p.Phe1313ProfsTer44). Parental segregation by Sanger sequencing proved that the variants were in trans. The parents were phenotypically healthy and had no proteinuria or hypoalbuminemia. Their serum creatinine was normal. The variants were not reported in control databases such as ClinVar, Genome aggregation database (gnomAD), Exome aggregation consortium (ExAC), Indian internal database (MedVarDb v3.0), and 1000 Genomes. The missense variant (LAMA5: c.385C > A) was predicted to be probably damaging by PolyPhen-2 Human divergence (HumDiv) and damaging by SIFT and LRT. Rare exome variant ensemble learner (REVEL) prediction score for the missense variant c.385C > A is deleterious (0.985). The variant prediction is deleterious by Varity (Deleterious (0.91)) and MutationTaster (Deleterious). The in silico predictions of the variant LAMA5 (NM_005560.6):c.3932_3936dup resulting in frameshift and premature truncation of the protein 44 amino acids downstream to codon 1313 (p.Phe1313ProfsTer44) was predicted to be damaging by MutationTaster2. The reference regions were conserved across the species for both the variants (combined annotation-dependent depletion (CADD) conservation score, 26.6 for missense variant and a conservation score of 7.826 by phyloP100 for truncating mutation). The variants have been classified as likely pathogenic and pathogenic, respectively, according to the American College of Medical Genetics (ACMG) 2015 nomenclature. All the CNS/DMS genes were checked and confirmed negative for pathogenic variants (WT1, PLCE1, NPHS1, NPHS2, LAMB2). There were no variants noted in other CNS genes.

Fig. 1
figure 1

a Light microscopy showing mesangial expansion in the absence of mesangial hypercellularity, thickened basement membrane, and decreased capillary lumen space (PAS stain). b Masson trichrome staining showing increase in mesangial matrix and segmental glomerulosclerosis and morphological features consistent with diffuse mesangial sclerosis

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Discussion

DMS has been reported previously in association with WT1, LAMB2, and PLCE1 gene mutations [1]; however, only one earlier report describes a LAMA5 variant causing DMS and nephrotic syndrome [2].

LAMA5 pathogenic gene variants with a phenotype of steroid resistant nephrotic syndrome are rare and have been identified in five pediatric cases so far, with only one case presenting as CNS [2,3,4,5]. Table 1 summarizes the clinical characteristics of pathogenic and likely pathogenic LAMA5 gene variants. Most of these are loss of function variants resulting in steroid resistant nephrotic syndrome or congenital nephrotic syndrome. LAMA5 gene has a significant number of benign missense variants reported in the literature. Braun et al. [3] reported homozygous missense variants of unknown significance at highly conserved residues in five pediatric patients with nephrotic syndrome from three consanguineous families using whole exome sequencing. Three of these patients were steroid sensitive and functional studies or pathologic analyses of these variants were not performed. Hence, the pathogenic role of these LAMA5 homozygous missense variants in causing nephrotic syndrome remains unclear.

Table 1 Clinical characteristics and genetic profile of pediatric patients with LAMA5 (NM_005560.6) gene and nephrotic syndrome in literature
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We identified new likely pathogenic variants in the LAMA5 gene clinically manifesting as CNS. A monogenic cause is predominant in CNS (69%). The NephQuest consortium study reports NPHS1, NPHS2, WT1 and PLCE1 as the commonly mutated genes in > 90% cases of CNS [1]. LAMA5 gene is a recently identified gene for CNS [2].

LAMA5, a crucial protein of laminin trimers, mediates crosstalk between the glomerular basement membrane (GBM) and podocytes [3, 5]. Our patient had isolated nephrotic syndrome in the absence of syndromic, extrarenal, or developmental defects probably due to defects confined to the GBM, and missense variants being milder might have led to a less severe phenotype. Taniguchi et al. [2] explained this phenotype using in vitro biochemical analysis of recombinant truncated Laminin α5 proteins. DMS is a distinct histological variant of nephrotic syndrome characterized by early onset and rapid progression to kidney failure; hypertension is noted in 78.6–86% of cases. Published cohort studies have identified PLCE or WT1 mutations in Isolated DMS (IDMS) [1]. Our patient is the second pediatric case of LAMA5 variant presenting with IDMS.

Our case adds LAMA5 gene to the constellation of genes causing DMS, in addition to the classically described WT1, LAMB2, and PLCE1 genes and to the list of genes causing CNS.

Summary

What is new?

  • Our case adds LAMA5 gene to the constellation of genes causing diffuse mesangial sclerosis (DMS), in addition to the classically described WT1, LAMB2, and PLCE1 genes and to the list of genes causing congenital nephrotic syndrome.