ZNF674: A New Krüppel-Associated Box–Containing Zinc-Finger Gene Involved in Nonsyndromic X-Linked Mental Retardation Dorien Lugtenberg, Helger G. Yntema,

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ZNF674: A New Krüppel-Associated Box–Containing Zinc-Finger Gene Involved in Nonsyndromic X-Linked Mental Retardation Dorien Lugtenberg, Helger G. Yntema, Martijn J.G. Banning, Astrid R. Oudakker, Helen V. Firth, Lionel Willatt, Martine Raynaud, Tjitske Kleefstra, Jean-Pierre Fryns, Hans-Hilger Ropers, Jamel Chelly, Claude Moraine, Jozef Gécz, Jeroen van Reeuwijk, Sander B. Nabuurs, Bert B.A. de Vries, Ben C.J. Hamel, Arjan P.M. de Brouwer, Hans van Bokhoven The American Journal of Human Genetics Volume 78, Issue 2, Pages 265-278 (February 2006) DOI: 10.1086/500306 Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 1 The index patient with the deletion on Xp11.3, at age 5 years and 9 mo. There were no specific dysmorphic features observed. The American Journal of Human Genetics 2006 78, 265-278DOI: (10.1086/500306) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 2 Array CGH profiles of the deletion in the index patient. A, X-chromosome array CGH profile of the index patient with a deletion in Xp11.3 of ∼1 Mb. B, Enlarged, detailed view of the 1-Mb deletion in Xp11.3. The X-axis displays the Mb position of the clones on the X chromosome, ordered from Xpter to Xqter on the basis of genomic position (see full-genome BAC rearrays at Genome Sciences Center Web site). Each dot represents the mean log2 transformed and less-normalized test-over-reference (T/R) intensity ratio for each clone (Y-axis). Clones are represented by six independent replica spots on the array. C, Schematic overview of the part of Xp11 that includes the deleted region and the zinc-finger gene cluster (UCSC Human Genome Browser). The deleted region is indicated (horizontal arrow), and all deleted genes are shown. For the zinc-finger gene cluster, all genes are shown, and a number of the neighboring genes are also depicted. The deletion was confirmed and fine mapped by duplex PCR analysis with primer sets inside and outside the deleted region. Cen = centromere; Tel = telomere; MQ = Milli Q. The American Journal of Human Genetics 2006 78, 265-278DOI: (10.1086/500306) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 3 Compositions of ZNF673 and ZNF674 and their proteins. A, Alignment of ZNF673 and ZNF674 amino acid sequences, showing very high homology for the KRAB A and B domains. In ZNF673, an early stop codon results in a protein without zinc-finger domains. The vertical line indicates the insertion of one adenine at position c.452 in exon 6 of ZNF673, resulting in the premature stop codon at position c.514. B, Schematic picture of the gene structure of ZNF673 and ZNF674. Coding sequence starts in exon 3. Exons 4 and 5 encode the KRAB A and B domains, respectively. In ZNF674, 11 zinc fingers are encoded by exon 6. Cen = centromere; Tel = telomere. C, The predicted ZNF674 protein. The positions of the amino acid changes are indicated. The 11 intact zinc-finger domains are represented by black boxes. The hatched box represents a degenerated pseudofinger that lacks one C residue, which is critical for the binding of a zinc atom. The American Journal of Human Genetics 2006 78, 265-278DOI: (10.1086/500306) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 4 Segregation analyses of the three nucleotide changes. Segregation of all nucleotide changes in families T040 (A), D008 (B), and P063 (C) are shown. A, The c.352G→T mutation was tested in all family members available. The proband is indicated with an arrow. PCR products were digested using FokI enzyme. From the wild-type DNA, three digestion products are formed that are 188, 169, and 132 bp in size. If the mutation is present, two products are formed that are 357 and 132 bp in size. B, For the segregation analysis of the c.1235C→A substitution, PCR products were sequenced for the proband (arrow), his mother, and an affected uncle. Conservation of the proline residue is indicated by a sequence alignment of all known zinc-finger genes in Xp11. C, In family P063, six family members were available for segregation analysis by direct sequencing, including the proband (arrow). Results are depicted for the tested family members. The American Journal of Human Genetics 2006 78, 265-278DOI: (10.1086/500306) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 5 Molecular modeling of p.P412L mutation in family D008. The DNA double helix is depicted as balls and sticks. The three adjacent zinc-finger domains consist of two β-sheets (arrows) and one α-helix (blue ribbon) per domain. Pink balls represent zinc atoms that are bound to the zinc-finger domains. The position of the mutated proline amino acid in the linker sequence between two zinc-finger domains is colored red. This figure was made using YASARA (see YASARA Web site). The American Journal of Human Genetics 2006 78, 265-278DOI: (10.1086/500306) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 6 Sequence alignments of ZNF674 protein. A, Complete tree of the sequence alignments from the position-specific iterated BLAST of the protein sequence of ZNF674 versus all human proteins. B, Phylogenetic subtree of 32 protein sequences, including all zinc-finger genes from the Xp11 cluster (gray boxes). C, Schematic representation of the genomic organization of the zinc-finger gene cluster on Xp11. Three paired sets were identified with the same orientation and a single zinc-finger gene (ZNF630). Each set includes a nonsyndromic XLMR gene present (ZNF41, ZNF81, or ZNF674). Cen = centromere; Tel = telomere. The American Journal of Human Genetics 2006 78, 265-278DOI: (10.1086/500306) Copyright © 2006 The American Society of Human Genetics Terms and Conditions