PMID: 29858904

Gene: PHEX

Disease: X-linked hypophosphatemic rickets

MonDO: 0010619

InheritancePattern: X- linked Dominant

CaseB:III-2: Male, 2 years onset, China

CasePresentingHPOs: HP:0004912, HP:0003109, HP:0003155, HP:0006505, HP:0002753, HP:0002982, HP:0004349, HP:0000944, HP:0011849, HP:0002970, HP:0003170 (Hypophosphatemic rickets, Hyperphosphaturia, Elevated alkaline phosphatase, Abnormality of limb epiphysis morphology, Thin cortices, Tibial bowing, Reduced bone mineral density, Abnormality of the metaphysis, Abnormal bone ossification, Genu varum, Abnormality of the acetabulum)

HPOsFreeText: Fuzzy structures

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is hemizygous for this mutation, Has a mother and grandmother with the same mutation/disease at 141.3 cm and 142.8 cm respectively

CasePreviousTesting: For all probands: Decreased serum phosphorus levels (0.64–0.9 mM; normal range, 1.29–1.94 mM), Increased 24-h urinary phosphorus levels (49.8–68.4 mmol/day; normal range, 12.9–42.0 mmol/day), Elevated blood alkaline phosphatase levels (350–668.7 U/L; normal range, 42–390 U/L), Lower limit of normal serum 1,25-dihydroxyvitamin D3 levels, Normal blood PTH, serum calcium levels and urine calcium/creatinine ratio, Elevated serum FGF23 (>1500 pg/mL; lower than 28 pg/mL in healthy family members)

CaseGenotypingMethod: Peripheral blood from the probands and affected family members was collected and genomic DNA extracted and quantified. Next-generation sequencing was performed on the probands following PCR amplification and the results were examined with the TruSight One Sequencing Panel, with such genes as PHEX, FGF23, SLC34A3, DMP1 and ENPP1. The mutations were then compared to a reference sequence and filtered for pathogenicity. Sanger sequencing was performed on the probands and family members to confirm the detected mutations.

Variant: NM_000444.5:c.433G>T (p.Glu145Ter)

CAID: CA412571205 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.433G%3ET

gnomAD: Not in gnomAD

CaseII-3: Female, 2 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970 (Hypophosphatemic rickets, Short stature, Genu varum)

HPOsFreeText: -2.09 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted novel, Daughter of II:II-2

CasePreviousTesting: Calcium levels (10.2 mg/dL), Decreased serum phosphate levels (2.1 mg/dL; reference 3.8-6.5), Elevated serum ALP (531 IU/L; reference 90-325), 25OHD3 levels (31.1 ng/ml), PTH levels (52.5 ng/L), TPR levels (62.3), Decreased TmP/GFR levels (1.31; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.979_983dup (p.His329Thrfs*4)

CAID: CA913187410 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187410

gnomAD: Not in gnomAD

CaseVII-3: Male, 4 years report, Turkey

CasePresentingHPOs: HP:0004912, HP:0002540, HP:0002970 (Hypophosphatemic rickets, Inability to walk, Genu varum)

HPOsFreeText: -3.44 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted de novo and confirmed by parental testing, Proband is hemizygous for this mutation, Mutation is at splice donor site at Intron 2

CasePreviousTesting: Calcium levels (9.0 mg/dL), Decreased serum phosphate levels (3.1 mg/dL; reference 3.8-6.5), Elevated serum ALP (393 IU/L; reference 90-325), 25OHD3 levels (4.9 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (154.7 ng/L), TPR levels (58.7), Decreased TmP/GFR levels (1.82; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5(PHEX):c.187+1G>T

CinVar: 438537 https://www.ncbi.nlm.nih.gov/clinvar/variation/438537/

gnomAD: Not in gnomAD

CaseII:II-2: Female, 37 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970, (Hypophosphatemic rickets, Short stature, Genu varum)

HPOsFreeText: -3.95 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted novel, Mother of II:II-3

CasePreviousTesting: Calcium levels (9.8 mg/dL), Decreased serum phosphate levels (2.1 mg/dL; reference 2.7-4.5), Normal serum ALP (111 IU/L; reference 41-120), 25OHD3 levels (10.5 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (73 ng/L), TPR levels (87), Decreased TmP/GFR levels (1.70; reference 2.2-3.6)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.979_983dup (p.His329Thrfs*4)

CAID: CA913187410 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187410

gnomAD: Not in gnomAD

CaseIV-3: Female, 5 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970 (Hypophosphatemic rickets, Short stature, Genu varum)

HPOsFreeText: -3.33 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted de novo and confirmed with parental testing, Variant is a splice donor-site mutation that skips exon 14

CasePreviousTesting: Calcium levels (9.4 mg/dL), Decreased serum phosphate levels (2.0 mg/dL; reference 3.7-5.6), Elevated serum ALP (559 IU/L; reference 90-325), 25OHD3 levels (28.3 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (138 ng/L), TPR levels (79.6), Decreased TmP/GFR levels (1.59; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.1586+2T>G

CAID: CA412575011 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.1586%2B2T%3EG

gnomAD: Not in gnomAD

CaseXIV-3: Female, 2.7 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970 (Hypophosphatemic rickets, Short stature, Genu varum)

HPOsFreeText: -2.01 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Proband's mother shares the mutation and disease, Variant is at a splice donor site in intron 12

CasePreviousTesting: Calcium levels (9.4 mg/dL), Decreased serum phosphate levels (2.2 mg/dL; reference 3.8-6.5), Elevated serum ALP (364 IU/L; reference 90-325), 25OHD3 levels (27 ng/ml), PTH levels (49 ng/L), TPR levels (75), Decreased TmP/GFR levels (1.65; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.1404+1del

CAID: CA913187413 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187413

gnomAD: Not in gnomAD

CaseIX-3: Male, 2.1 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0002970 (Hypophosphatemic rickets, Genu varum)

HPOsFreeText: -0.75 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Proband is hemizyogus for this mutation, Variant is a splice donor site at intron 4

CasePreviousTesting: Calcium levels (10.1 mg/dL), Decreased serum phosphate levels (2.6 mg/dL; reference 3.8-6.5), Elevated serum ALP (827 IU/L; reference 90-325), 25OHD3 levels (32.3 ng/ml), PTH levels (107.1 ng/L), TPR levels (74), Decreased TmP/GFR levels (1.92; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.436+1G>T

CAID: CA412571215 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.436%2B1G%3ET

gnomAD: Not in gnomAD

CaseXV-3: Female, 3.3 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970 (Hypophosphatemic rickets, Short stature, Genu varum)

HPOsFreeText: -3.04 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is de novo and is confirmed by parental testing

CasePreviousTesting: Calcium levels (9.4 mg/dL), Decreased serum phosphate levels (2.9 mg/dL; reference 3.8-6.5), Elevated serum ALP (677 IU/L; reference 90-325), 25OHD3 levels (107 ng/ml), 1,25(OH)2D3 levels (54.2 pg/mL), PTH levels (79.3 ng/L), TPR levels (83.4), Decreased TmP/GFR levels (2.8; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.1206del (p.Gln402Hisfs*6)

CAID: CA913187414 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187414

gnomAD: Not in gnomAD

CaseVI-4: Male, 3.5 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0002540, HP:0002970 (Hypophosphatemic rickets, Inability to walk, Genu varum)

HPOsFreeText: -3.76 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted de novo and confirmed by parental testing, Proband is hemizygous for this mutation

CasePreviousTesting: Calcium levels (9.8 mg/dL), Decreased serum phosphate levels (2.8 mg/dL; reference 3.8-6.5), Elevated serum ALP (925 IU/L; reference 90-325), 25OHD3 levels (35 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (62.2 ng/L), TPR levels (69.7), Decreased TmP/GFR levels (1.95; reference 2.9-6.1)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.1217G>T (p.Cys406Phe)

CAID: CA412573391 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.1217G%3ET

gnomAD: Not in gnomAD

NonPatientCell: EFO:0001182 (HEK293 Cells)

GeneFunction: GO:0008233 (Peptidase activity)

GeneAlteration: HEK293 cells were grown and 8 missense mutations were identified and generated by PCR-mutagenesis. The human mutant cDNAs were transfected into the cells using the calcuim-phosphate coprecipitation method and examined.

FunctionalEvidence: When HEK293 cells were transfected with wild-type and mutant human cDNA for PHEX, the resulting cells were subject to immunoblotting to determine the protein levels in both the cell lysate and the media of cells. All the variants and the wild-type showed presence in the lysate at various levels, but C85R, G579R, G579V, S711R, and A720T were all devoid of any secreted protein in the media. Ananlysis of these cells also showed possible rescue by growing transfected cells at 26 C, thus glycosylating and maturing the proteins. The endopeptidase activity of the wild-type and variants were also compared, with D237G and Y317F mutant proteins exhibiting 50–60% of wild-type activity; E581V and S711R also displayed nearly undetectable activity. This displayed that the disease causing mechanism could be related to loss of function of peptidase activity or cellular trafficking. Evidence is found under "Results".

FAVariant1: NM_000444.5:c.253T>C (p.Cys85Arg)

ClinVar: 438549 https://www.ncbi.nlm.nih.gov/clinvar/variation/438549/

FAVariant2: NM_000444.5:c.1735G>A (p.Gly579Arg)

ClinVar: 226119 https://www.ncbi.nlm.nih.gov/clinvar/variation/226119/

FAVariant3: NM_000444.5:c.1736G>T (p.Gly579Val)

ClinVar: 372777 https://www.ncbi.nlm.nih.gov/clinvar/variation/372777/

FAVariant4: NM_000444.5:c.2131A>C (p.Ser711Arg)

CAID: CA412575294 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA412575294

FAVariant5: NM_000444.5:c.2158G>A (p.Ala720Thr)

CAID: CA412575364 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA412575364