BRIEF REPORT OFFICIAL JOURNAL www.hgvs.org Evidence Against RAB40AL Being the Locus for Martin–Probst X-Linked Deafness–Intellectual Disability Syndrome Monika Oldak, 1,2 ∗ Aneta ´ Scie˙ zy´ nska, 1 Wojciech Mlynarski, 3 Maciej Borowiec, 3,4 Ewelina Ruszkowska, 1 Kamil Szulborski, 5 Agnieszka Pollak, 2 Joanna Kosi ´ nska, 6 Malgorzata Mueller-Malesi ´ nska, 2 Piotr Stawi ´ nski, 2 Jacek P. Szaflik, 5 and Rafal Ploski 2,6 ∗ 1 Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland; 2 Institute of Physiology and Pathology of Hearing, Warsaw, Poland; 3 Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland; 4 Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland; 5 Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland; 6 Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland Communicated by Richard Gibbs Received 4 April 2014; accepted revised manuscript 2 July 2014. Published online 18 July 2014 in Wiley Online Library (www.wiley.com/humanmutation). DOI: 10.1002/humu.22620 ABSTRACT: RAB40AL has been reported as the locus for Martin–Probst syndrome (MPS), an X-linked deafness– intellectual disability syndrome. The report was based on segregation of a missense change p.D59G with the dis- ease in a single family and in vitro localization studies. We found the p.D59G variant by whole-exome sequenc- ing in two patients; however, the diagnosis of MPS was excluded in both cases. Furthermore, screening of control DNA samples (n = 810) from a general Polish popula- tion, using allele-specific PCR and direct DNA sequenc- ing for verification, identified p.D59G in 8/405 males and 12/405 females. High prevalence of the p.D59G variant (2.47%) is typical for a common genetic variation ob- served in asymptomatic individuals. Our data question the role of RAB40AL mutation as a disease-causing change and the involvement of RAB40AL in MPS. Considering an increasing use of next-generation sequencing in the clinical setting, our finding is of practical diagnostic im- portance. Hum Mutat 35:1171–1174, 2014. C  2014 Wiley Periodicals, Inc. KEY WORDS: whole-exome sequencing; intellectual disabil- ity; deafness; Martin–Probst syndrome; RAB40AL; non- pathogenic Martin–Probst syndrome (MPS) was described as a recessive X- linked syndrome characterized by the presence of cognitive im- pairment, progressive sensorineural hearing loss, facial dysmor- phism, and variable other features including short stature, mi- ∗ Correspondence to: Monika Oldak, Department of Histology and Embryology, Cen- ter of Biostructure Research, Medical University of Warsaw, Chalubi ´ nskiego 5, Warsaw 02-004, Poland. E-mail: Monika.Oldak@wum.edu.pl; Rafal Ploski, Department of Medi- cal Genetics, Medical University of Warsaw, Pawi ´ nskiego 3c, Warsaw 02-016, Poland. E-mail: rploski@wp.pl Contract grant sponsors: National Science Center (NN402591540 [5915/B/P01/2011/40] and 2011/01/M/NZ5/02815); European Commission Seventh Framework Programme (FP7-REGPOT-2012-CT2012-316254-BASTION). crocephaly, widely spaced, hypoplastic nipples, abnormal dermato- glyphics, and late-onset pancytopenia [Martin et al., 2000]. Recently, MPS has been reported to be caused by the dinucleotide substitution c.176 177delACinsGA in RAB40AL (MIM #300405; NG 017150.1). These data represented the first association of RAB40AL mutation with a human disorder. However, so far, there have been no other studies confirming RAB40AL as the MPS locus. RAB40AL encodes a 278-amino-acid mitochondrial protein, which has an unknown function and is expressed mainly in the brain and kidney [Saito- Ohara et al., 2002; Bedoyan et al., 2012]. The c.176 177delACinsGA is predicted to cause a replace- ment of aspartic acid by glycine (GAC>GGA) at codon 59 (p.D59G, NP 001027004.1). This variant can also be de- scribed as NM 001031834.1:c.176A>G transition (rs145606134), co-occurring with an NM 001031834.1:c.177C>A transversion (rs138133927). In the present study, we have identified RAB40AL:c.176 177delACinsGA in two unrelated Polish males who underwent whole-exome sequencing (WES) for clinical purposes (Fig. 1A– C). RAB40AL gene maps to chromosome X and both patients were hemizygous for the variant. Patients and examined family members gave written consent and the study was approved by the local Ethics Committees. Genomic DNA was extracted from blood. WES was performed as previously described using HiSeq 1500 (Illumina, San Diego, CA) [Ploski et al., 2014]. The presence of the RAB40AL vari- ant was confirmed by direct DNA sequencing (ABI PRISM 3500XL sequencer; Applied Biosystems, Foster City, CA). The index patient of family 1 was a 53-year-old male diagnosed with optic atrophy at the age of 47. Except for the proband, four of his seven sons were affected. He was found to carry an OPA1 gene mu- tation (NM 130837.2:c.1035+5G>A), which segregated with visual problems in the family (Fig. 1A). After a comprehensive audiological assessment, a mild-to-moderate sensorineural hearing impairment was observed only at higher frequencies, that is, from 4 kHz in the left ear and from 12.5 kHz in the right ear. The patient did not complain of hearing difficulties. He has neither dysmorphic facial features, birth defects, intellectual impairment, nor hematopoietic dysfunction. His height is 182 cm (90 th centile) and head circum- ference 56.5 cm (50 th centile). In the second family, the index patient is a 6-year-old male who has a different phenotype than the first index patient. At his first hos- pital admission at the age of 8 weeks, he presented with recurrent C  2014 WILEY PERIODICALS, INC.