DFNX1 Nonsyndromic Hearing Loss and Deafness – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY
Synonym: DFN2 Nonsyndromic Hearing Loss and Deafness
Xue Z Liu, MD, PhD, Huijun Yuan, MD, PhD, Rahul Mittal, PhD, and Denise Yan, PhD.
Author Information and AffiliationsInitial Posting: August 4, 2011; Last Update: July 19, 2018.
Estimated reading time: 14 minutes
Summary
NOTE: THIS PUBLICATION HAS BEEN RETIRED. THIS ARCHIVAL VERSION IS FOR HISTORICAL REFERENCE ONLY, AND THE INFORMATION MAY BE OUT OF DATE.
Clinical characteristics.
DFNX1 nonsyndromic hearing loss and deafness is part of the spectrum of PRPS1-related disorders. Hearing loss in hemizygous males is bilateral, sensorineural, and moderate to profound; prelingual or postlingual in onset; and progressive or non-progressive. The audiogram shape is variable. Hearing in female carriers can be normal or abnormal.
Diagnosis/testing.
Diagnosis relies on the presence of characteristic hearing loss in males and detection of a hemizygous PRPS1 pathogenic variant.
Management.
Treatment of manifestations: Routine management of sensorineural hearing loss. Cochlear implantation can improve auditory and oral communication skills in affected males.
Surveillance: Regular audiologic evaluation to assess hearing status and progression of hearing loss.
Evaluation of relatives at risk: Evaluate at-risk males at birth with detailed audiometry to assure early diagnosis and treatment of hearing loss.
Genetic counseling.
DFNX1 is inherited in an X-linked manner. The father of an affected male will not have the disorder nor will he be a carrier of the pathogenic variant. If the mother of an affected male has a pathogenic variant, the chance of transmitting it in each pregnancy is 50%. Males who inherit the variant will be affected; females who inherit the variant will be carriers and may have hearing loss. Carrier testing for at-risk female relatives, prenatal testing for a pregnancy at increased risk, and preimplantation genetic testing are possible if the PRPS1 pathogenic variant in the family has been identified.
Diagnosis
Suggestive Findings
DFNX1 nonsyndromic hearing loss and deafness, part of the spectrum of PRPS1-related disorders, should be considered in a male proband with the following clinical, laboratory, and imaging findings and family history.
Clinical findings
Sensorineural hearing loss is:
Bilateral moderate to profound;
Prelingual or postlingual in onset;
Progressive or non-progressive.
Audiograms are usually flat across all frequencies. However, some individuals have severe hearing loss in the low frequencies and some have residual hearing in the high frequencies.
Vestibular function is normal.
Imagining. Temporal bone imaging is normal.
Family history is consistent with X-linked inheritance. In heterozygous females hearing can be normal or abnormal.
Establishing the Diagnosis
Male proband. The diagnosis of DFNX1 is established in a male proband with sensorineural hearing loss and a hemizygous pathogenic variant in PRPS1 identified by molecular genetic testing [Liu et al 2010, Kim et al 2016] (see Table 1).
Female carrier. The diagnosis of DFNX1 is usually established in a female carrier who may have normal hearing or sensorineural hearing loss and a heterozygous pathogenic variant in PRPS1 identified by molecular genetic testing [Liu et al 2010] (see Table 1).
Molecular genetic testing. Because the phenotype of DFNX1 is indistinguishable from many other inherited disorders with hearing loss, recommended molecular genetic testing approaches include use of a multigene panel (see Option 1) or comprehensive genomic testing (see Option 2).
Note: Single-gene testing (sequence analysis of PRPS1 followed by gene-targeted deletion/duplication analysis) is rarely useful and typically NOT recommended.
Option 1
A multigene panel that includes PRPS1 and other genes of interest (see Hereditary Hearing Loss and Deafness Overview) is most likely to identify the genetic cause of the condition while limiting identification of variants of uncertain significance and pathogenic variants in genes that do not explain the underlying phenotype. Note: (1) The genes included in the panel and the diagnostic sensitivity of the testing used for each gene vary by laboratory and are likely to change over time. (2) Some multigene panels may include genes not associated with the condition discussed in this GeneReview. Of note, given the rarity of DFNX1 nonsyndromic hearing loss and deafness some panels for hearing loss may not include this gene. (3) In some laboratories, panel options may include a custom laboratory-designed panel and/or custom phenotype-focused exome analysis that includes genes specified by the clinician. (4) Methods used in a panel may include sequence analysis, deletion/duplication analysis, and/or other non-sequencing-based tests.
For an introduction to multigene panels click here. More detailed information for clinicians ordering genetic tests can be found here.
Option 2
Comprehensive genomic testing (which does not require the clinician to determine which gene[s] are likely involved) is another good option. Exome sequencing is most commonly used; genome sequencing is also possible.
Exome array (when clinically available) may be considered if exome sequencing is not diagnostic.
For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.
Table 1.
Molecular Genetic Testing Used in DFNX1
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| Gene 1 | Method | Proportion of Pathogenic Variants 2 Detectable by Method |
|---|
|
PRPS1
| Sequence analysis 3 | 5/5 4 |
| Gene-targeted deletion/duplication analysis 5 | Unknown 6 |
- 1.
- 2.
- 3.
- 4.
Sequencing of the seven exons of the coding region and the intron/exon boundaries of PRPS1 in the five families reported to date with DFNX1 nonsyndromic hearing loss and deafness identified five different pathogenic missense variants [Liu et al 2010, Kim et al 2016]. To date no intragenic deletions or duplications have been observed.
- 5.
Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include a range of techniques such as quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications.
- 6.
Clinical Characteristics
Clinical Description
Hearing loss in individuals with DFNX1 nonsyndromic hearing loss and deafness can be prelingual or postlingual (in which onset ranges from 3 years to 20 years), progressive or non-progressive, and severe to profound [Liu et al 2010, Liu et al 2013, Kim et al 2016].
Synofzik et al [2014] concluded that the three PRPS1-related phenotypes (CMTX5, Arts syndrome, and DFNX1) constitute a continuum after observing all three phenotypes in one family with a loss-of-function pathogenic variant: a male with CMT and Arts syndrome and a heterozygous female with hearing loss due to skewing of X-chromosome inactivation. On detailed clinical and neurophysiologic examination manifestations of peripheral neuropathy that range from a subclinical axonal motor neuropathy to an axonal sensory-motor neuropathy were found in males with PRPS1-related hearing loss [Robusto et al 2015]. In addition, optic atrophy and retinitis pigmentosa have been described in females heterozygous for a PRPS1 pathogenic variant [Almoguera et al 2014].
Heterozygous females. Hearing in heterozygous females can be normal or abnormal. When hearing is abnormal, hearing loss can be either symmetric or asymmetric and ranges from mild to moderate [Liu et al 2013].
In the family described by Almoguera et al [2014], both the proband and her mother have peripheral neuropathy and ophthalmologic manifestations, whereas the phenotype of the affected sister is milder and confined to eye, with no hearing loss.
Genotype-Phenotype Correlations
The established PRPS1-related disorders are not distinct entities, but rather clusters on a phenotypic continuum as evidenced by overlap of the features of CMTX5 / Arts syndrome / DFNX1 both in affected individuals and within families. A wide and continuous spectrum of clinical manifestations has been associated with PRPS1 missense variants (see Genetically Related Disorders). A relationship between the type (location) of PRS-I disruption and phenotype has been suggested, with the most severe phenotypes caused by variants predicted to affect allosteric and active sites and the milder phenotypes caused by variants predicted to disrupt the structure locally [de Brouwer et al 2010].
In females, who predictably have a less severe presentation, the ratio of X chromosome inactivation adds an additional variable in predicting clinical outcome [Synofzik et al 2014].
Management
Evaluations Following Initial Diagnosis
To establish the extent of disease and needs of an individual diagnosed with DFNX1 nonsyndromic hearing loss and deafness, the evaluations summarized in this section (if not performed as part of the evaluation that led to the diagnosis) are recommended:
Pure tone audiograms, auditory brain stem response testing
Evaluation for peripheral neuropathy and ophthalmologic findings (optic atrophy and retinitis pigmentosa)
Consultation with a clinical geneticist and/or genetic counselor
Surveillance
Hearing loss in DFNX1 is prelingual or postlingual and progressive; regular audiologic evaluation is recommended to assess hearing status and progression of hearing loss.
Periodic reevaluation of clinical findings by a neurologist is indicated for males with clinical evidence of peripheral neuropathy.
Evaluation of Relatives at Risk
Determining in infancy whether at-risk male and female relatives of a person with DFNX1 nonsyndromic hearing loss and deafness have inherited the PRPS1 pathogenic variant allows for early support and management of the child and the family.
Evaluations may include:
See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.
Therapies Under Investigation
Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Genetic Counseling
Genetic counseling is the process of providing individuals and families with
information on the nature, mode(s) of inheritance, and implications of genetic disorders to help them
make informed medical and personal decisions. The following section deals with genetic
risk assessment and the use of family history and genetic testing to clarify genetic
status for family members; it is not meant to address all personal, cultural, or
ethical issues that may arise or to substitute for consultation with a genetics
professional. —ED.
Mode of Inheritance
DFNX1 nonsyndromic hearing loss and deafness is inherited in an X-linked manner.
Risk to Family Members
Parents of a male proband
In a family with more than one affected individual, the mother of an affected male is an
obligate heterozygote (
carrier). Note: If a woman has more than one affected child and no other affected relatives and if the
PRPS1 pathogenic variant cannot be detected in her leukocyte DNA, she most likely has
germline mosaicism. Although maternal germline mosaicism has not been reported to date, it remains a possibility.
If a male is the only affected family member (i.e., a
simplex case), the mother may be a
heterozygote or the affected male may have a
de novo
PRPS1 pathogenic variant, in which case the mother is not a heterozygote. The frequency of
de novo pathogenic variants is not known.
Sibs of a male proband. The risk to sibs depends on the genetic status of the mother:
If the mother of the
proband has the
PRPS1 pathogenic variant, the chance of transmitting it in each pregnancy is 50%. Intrafamilial clinical variability has been reported.
Females who inherit the variant will be heterozygotes and may be unaffected, have nonsyndromic hearing loss, or have peripheral neuropathy and optic atrophy, as well as retinitis pigmentosa (RP) as the only manifestations [
Almoguera et al 2014].
Offspring of a male proband. Males with DFNX1 transmit the PRPS1 pathogenic variant to:
All of their daughters, who will be heterozygotes and may be unaffected, have nonsyndromic hearing loss, or have peripheral neuropathy and optic atrophy and RP as the only manifestations [
Almoguera et al 2014];
None of their sons.
Other family members. A male proband's maternal aunts and maternal cousins may be heterozygous or hemizygous (depending on their sex) and have a range of clinical manifestations [Almoguera et al 2014, Gandía et al 2015, Robusto et al 2015].
Note: Molecular genetic testing may be able to identify the family member in whom a de novo pathogenic variant arose, information that could help determine genetic risk status of the extended family.
Heterozygote Detection
Molecular genetic testing of female relatives to determine their genetic status requires prior identification of the PRPS1 pathogenic variant in the proband.
Note: Females who are heterozygotes for a PRPS1 pathogenic variant may be unaffected, develop hearing loss (reported findings included either symmetric or asymmetric hearing loss that varied from mild to moderate in degree [Liu et al 2013]), or have peripheral neuropathy and optic atrophy, retinitis pigmentosa RP as the only manifestations [Almoguera et al 2014].
Prenatal Testing and Preimplantation Genetic Testing
Once the PRPS1 pathogenic variant has been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic testing for DFNX1 nonsyndromic hearing loss and deafness are possible. Note: Prenatal genetic testing results cannot be used to reliably predict the phenotype as intrafamilial variability has been reported.
Differences in perspective may exist among medical professionals and within families regarding the use of prenatal testing. While most centers would consider use of prenatal testing to be a personal decision, discussion of these issues may be helpful.
Resources
GeneReviews staff has selected the following disease-specific and/or umbrella
support organizations and/or registries for the benefit of individuals with this disorder
and their families. GeneReviews is not responsible for the information provided by other
organizations. For information on selection criteria, click here.
Medical Home Portal
Alexander Graham Bell Association for the Deaf and Hard of Hearing
Phone: 866-337-5220 (toll-free); 202-337-5221 (TTY)
Fax: 202-337-8314
Email: info@agbell.org
American Society for Deaf Children
Phone: 800-942-2732 (ASDC)
Email: info@deafchildren.org
BabyHearing.org
This site, developed with support from the National Institute on Deafness and Other Communication Disorders, provides information about newborn hearing screening and hearing loss.
MedlinePlus
National Association of the Deaf
Phone: 301-587-1788 (Purple/ZVRS); 301-328-1443 (Sorenson); 301-338-6380 (Convo)
Fax: 301-587-1791
Email: nad.info@nad.org
Molecular Genetics
Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.
Table A.
DFNX1 Nonsyndromic Hearing Loss and Deafness: Genes and Databases
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Data are compiled from the following standard references: gene from
HGNC;
chromosome locus from
OMIM;
protein from UniProt.
For a description of databases (Locus Specific, HGMD, ClinVar) to which links are provided, click
here.
Gene structure.
PRPS1 spans approximately 23 kb with seven exons. See Table A, Gene for a detailed summary of gene and protein information.
Pathogenic variants. Five missense variants in PRPS1 have been associated with DFNX1 (see Table 4). These variants have been shown to result in reduced enzyme activity [Liu et al 2010, Kim et al 2016].
Table 4.
Selected PRPS1 Pathogenic Variants
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| DNA Nucleotide Change | Predicted Protein Change | Reference Sequences |
|---|
| c.193G>A | p.Asp65Asn |
NM_002764.3
NP_002755.1
|
| c. 244G>C | p.Ala82Pro |
| c.259G>A | p.Ala87Thr |
| c.869T>C | p.Ile290Thr |
| c.916G>A | p.Gly306Arg |
Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.
Normal gene product.
PRPS1 encodes a 318-amino acid protein, the PRS-I (ribose-phosphate pyrophosphokinase 1) enzyme. The active unit is a hexamer that consists of a trimer of homodimers. The enzyme catalyzes the phosphoribosylation of ribose 5-phosphate from adenosine triphosphate (ATP) to 5-phosphoribosyl-1-pyrophosphate, which is necessary for the de novo and salvage pathways of purine and pyrimidine biosynthesis. This enzyme is activated by inorganic Mg+2 but can be allosterically inhibited by adenosine diphosphate (ADP) and purines.
Phosphoribosylpyrophosphate synthetase (PRS) I enzyme activity can be analyzed in fibroblasts, lymphoblasts, and erythrocytes [Torres et al 1996, de Brouwer et al 2007, Kim et al 2007, Kim et al 2016] using high-performance liquid chromatography measurement of AMP; however, this assay is not currently part of routine care.
Abnormal gene product. Despite disease-associated variants resulting in loss of PRS-I enzyme activity, as evidenced by decreased enzyme activity in erythrocytes and cultured fibroblasts from males with DFNX1, all reported disease-associated variants are misssense changes [Liu et al 2010]. Pathogenic variants causing reduced enzyme activity either reduce stability of PRS-I or moderately affect interactions in the trimer interface. The lack of affected males in the family reported by Almoguera et al [2014] suggests that some causative variants are lethal in hemizygotes.
Interestingly, computer-assisted molecular modeling showed that pathogenic variants causing Arts syndrome and CMTX5 disturb the ATP binding site of PRS-I suggesting that these syndromes are caused by pathogenic variants predicted to affect allosteric and active sites (see Genotype-Phenotype Correlations).
Of note, pathogenic variants that result in PRS superactivity disturb either one or both allosteric sites involved in the inhibition of PRS-I enzyme activity by ADP or purine binding (see Genetically Related Disorders). Variants reported to be associate with superactivity have been reported from amino acid 52 to 192.
Chapter Notes
Revision History
19 July 2018 (bp) Comprehensive update posted live
4 August 2011 (me) Review posted live
31 March 2011 (xzl) Original submission
References
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