Recurrent CNVs and SNVs at the NPHP1 Locus Contribute Pathogenic Alleles to Bardet-Biedl Syndrome

Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1, a known...

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Published inAmerican journal of human genetics Vol. 94; no. 5; pp. 745 - 754
Main Authors Lindstrand, Anna, Davis, Erica E., Carvalho, Claudia M.B., Pehlivan, Davut, Willer, Jason R., Tsai, I-Chun, Ramanathan, Subhadra, Zuppan, Craig, Sabo, Aniko, Muzny, Donna, Gibbs, Richard, Liu, Pengfei, Lewis, Richard A., Banin, Eyal, Lupski, James R., Clark, Robin, Katsanis, Nicholas
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 01.05.2014
Cell Press
Elsevier
Subjects
Adaptor Proteins, Signal Transducing - genetics
Alleles
Animals
Bardet-Biedl Syndrome - genetics
Danio rerio
DNA Copy Number Variations
Gastrulation - genetics
Genetic Loci
Genomics
Genotype & phenotype
Heterozygote
Homozygote
Humans
Kidney - abnormalities
Membrane Proteins - genetics
Mice
Mutation
Pedigree
Rodents
Sequence Deletion
Zebrafish - abnormalities
Zebrafish - genetics
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Abstract Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1, a known JBTS locus. Given these observations, we investigated the contribution of NPHP1 in Bardet-Biedl syndrome (BBS), a ciliopathy of intermediate severity. By using a combination of array-comparative genomic hybridization, TaqMan copy number assays, and sequencing, we studied 200 families affected by BBS. We report a homozygous NPHP1 deletion CNV in a family with classical BBS that is transmitted with autosomal-recessive inheritance. Further, we identified heterozygous NPHP1 deletions in two more unrelated persons with BBS who bear primary mutations at another BBS locus. In parallel, we identified five families harboring an SNV in NPHP1 resulting in a conserved missense change, c.14G>T (p.Arg5Leu), that is enriched in our Hispanic pedigrees; in each case, affected individuals carried additional bona fide pathogenic alleles in another BBS gene. In vivo functional modeling in zebrafish embryos demonstrated that c.14G>T is a loss-of-function variant, and suppression of nphp1 in concert with each of the primary BBS loci found in our NPHP1-positive pedigrees exacerbated the severity of the phenotype. These results suggest that NPHP1 mutations are probably rare primary causes of BBS that contribute to the mutational burden of the disorder.
AbstractList Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1, a known JBTS locus. Given these observations, we investigated the contribution of NPHP1 in Bardet-Biedl syndrome (BBS), a ciliopathy of intermediate severity. By using a combination of array-comparative genomic hybridization, TaqMan copy number assays, and sequencing, we studied 200 families affected by BBS. We report a homozygous NPHP1 deletion CNV in a family with classical BBS that is transmitted with autosomal-recessive inheritance. Further, we identified heterozygous NPHP1 deletions in two more unrelated persons with BBS who bear primary mutations at another BBS locus. In parallel, we identified five families harboring an SNV in NPHP1 resulting in a conserved missense change, c.14G>T (p.Arg5Leu), that is enriched in our Hispanic pedigrees; in each case, affected individuals carried additional bona fide pathogenic alleles in another BBS gene. In vivo functional modeling in zebrafish embryos demonstrated that c.14G>T is a loss-of-function variant, and suppression of nphp1 in concert with each of the primary BBS loci found in our NPHP1-positive pedigrees exacerbated the severity of the phenotype. These results suggest that NPHP1 mutations are probably rare primary causes of BBS that contribute to the mutational burden of the disorder.
Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1 , a known JBTS locus. Given these observations, we investigated the contribution of NPHP1 in Bardet-Biedl syndrome (BBS), a ciliopathy of intermediate severity. By using a combination of array-comparative genomic hybridization, Taq Man copy number assays, and sequencing, we studied 200 families affected by BBS. We report a homozygous NPHP1 deletion CNV in a family with classical BBS that is transmitted with autosomal-recessive inheritance. Further, we identified heterozygous NPHP1 deletions in two more unrelated persons with BBS who bear primary mutations at another BBS locus. In parallel, we identified five families harboring an SNV in NPHP1 resulting in a conserved missense change, c.14G>T (p.Arg5Leu), that is enriched in our Hispanic pedigrees; in each case, affected individuals carried additional bona fide pathogenic alleles in another BBS gene. In vivo functional modeling in zebrafish embryos demonstrated that c.14G>T is a loss-of-function variant, and suppression of nphp1 in concert with each of the primary BBS loci found in our NPHP1 -positive pedigrees exacerbated the severity of the phenotype. These results suggest that NPHP1 mutations are probably rare primary causes of BBS that contribute to the mutational burden of the disorder.
Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1, a known JBTS locus. Given these observations, we investigated the contribution of NPHP1 in Bardet-Biedl syndrome (BBS), a ciliopathy of intermediate severity. By using a combination of array-comparative genomic hybridization, TaqMan copy number assays, and sequencing, we studied 200 families affected by BBS. We report a homozygous NPHP1 deletion CNV in a family with classical BBS that is transmitted with autosomal-recessive inheritance. Further, we identified heterozygous NPHP1 deletions in two more unrelated persons with BBS who bear primary mutations at another BBS locus. In parallel, we identified five families harboring an SNV in NPHP1 resulting in a conserved missense change, c.14G>T (p.Arg5Leu), that is enriched in our Hispanic pedigrees; in each case, affected individuals carried additional bona fide pathogenic alleles in another BBS gene. In vivo functional modeling in zebrafish embryos demonstrated that c.14G>T is a loss-of-function variant, and suppression of nphp1 in concert with each of the primary BBS loci found in our NPHP1-positive pedigrees exacerbated the severity of the phenotype. These results suggest that NPHP1 mutations are probably rare primary causes of BBS that contribute to the mutational burden of the disorder. [PUBLICATION ABSTRACT]
Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic interval has also been detected in individuals with Joubert syndrome (JBTS), and in the mouse, Nphp1 interacts genetically with Ahi1, a known JBTS locus. Given these observations, we investigated the contribution of NPHP1 in Bardet-Biedl syndrome (BBS), a ciliopathy of intermediate severity. By using a combination of array-comparative genomic hybridization, TaqMan copy number assays, and sequencing, we studied 200 families affected by BBS. We report a homozygous NPHP1 deletion CNV in a family with classical BBS that is transmitted with autosomal-recessive inheritance. Further, we identified heterozygous NPHP1 deletions in two more unrelated persons with BBS who bear primary mutations at another BBS locus. In parallel, we identified five families harboring an SNV in NPHP1 resulting in a conserved missense change, c.14G>T (p.Arg5Leu), that is enriched in our Hispanic pedigrees; in each case, affected individuals carried additional bona fide pathogenic alleles in another BBS gene. In vivo functional modeling in zebrafish embryos demonstrated that c.14G>T is a loss-of-function variant, and suppression of nphp1 in concert with each of the primary BBS loci found in our NPHP1-positive pedigrees exacerbated the severity of the phenotype. These results suggest that NPHP1 mutations are probably rare primary causes of BBS that contribute to the mutational burden of the disorder.
Author Carvalho, Claudia M.B.
Davis, Erica E.
Zuppan, Craig
Katsanis, Nicholas
Lewis, Richard A.
Ramanathan, Subhadra
Muzny, Donna
Clark, Robin
Lindstrand, Anna
Tsai, I-Chun
Willer, Jason R.
Sabo, Aniko
Banin, Eyal
Gibbs, Richard
Lupski, James R.
Liu, Pengfei
Pehlivan, Davut
AuthorAffiliation 2 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
7 Center for Retinal and Macular Degenerations, Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
4 Division of Medical Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
6 Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
8 Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX 77030, USA
5 Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA 92359, USA
1 Center for Human Disease Modeling, Duke University School of Medicine, Durham, NC 27710, USA
3 Centro de Pesquisas René Rachou – FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/24746959$$D View this record in MEDLINE/PubMed
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Copyright 2014 The American Society of Human Genetics
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Copyright Cell Press May 1, 2014
2014 The American Society of Human Genetics. Published by Elsevier Ltd. All right reserved. 2014 The American Society of Human Genetics
Copyright_xml – notice: 2014 The American Society of Human Genetics
– notice: Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
– notice: Copyright Cell Press May 1, 2014
– notice: 2014 The American Society of Human Genetics. Published by Elsevier Ltd. All right reserved. 2014 The American Society of Human Genetics
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Present address: Department of Molecular Medicine & Surgery, Karolinska Institute, 17176 Stockholm, Sweden
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Snippet Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic...
Homozygosity for a recurrent 290 kb deletion of NPHP1 is the most frequent cause of isolated nephronophthisis (NPHP) in humans. A deletion of the same genomic...
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SubjectTerms Adaptor Proteins, Signal Transducing - genetics
Alleles
Animals
Bardet-Biedl Syndrome - genetics
Danio rerio
DNA Copy Number Variations
Gastrulation - genetics
Genetic Loci
Genomics
Genotype & phenotype
Heterozygote
Homozygote
Humans
Kidney - abnormalities
Membrane Proteins - genetics
Mice
Mutation
Pedigree
Rodents
Sequence Deletion
Zebrafish - abnormalities
Zebrafish - genetics
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Title Recurrent CNVs and SNVs at the NPHP1 Locus Contribute Pathogenic Alleles to Bardet-Biedl Syndrome
URI https://dx.doi.org/10.1016/j.ajhg.2014.03.017
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