Total 60 pathogenic variants reported for Phytanic acid storage disease 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_006214.4(PHYH):c.823C>T (p.Arg275Trp) SNV
Germline		 Chr10:13283695 Pathogenic/Likely pathogenic REFSUM DISEASE, ADULT, 1
Condition: not provided
Retinitis pigmentosa
Phytanic acid storage disease
Inborn genetic diseases		 Criteria Provided
Multiple Submitters
No Conflicts
 CA118904 rs_104894178

15 SubmittersRCV000008018RCV000255609RCV000505105RCV000665657RCV002426496
NM_006214.4(PHYH):c.135-2A>G SNV
Germline		 Chr10:13295608 Pathogenic REFSUM DISEASE, ADULT, 1
Condition: not provided
Phytanic acid storage disease
Retinitis pigmentosa
PHYH-related disorder
Uterine corpus endometrial carcinoma
Clear cell carcinoma of kidney
Thyroid cancer, nonmedullary, 1
Retinal dystrophy
Acute myeloid leukemia
Familial cancer of breast		 Criteria Provided
Multiple Submitters
No Conflicts
 CA212871 rs_201578674

13 SubmittersRCV000008019RCV000599568RCV000660487RCV001723551RCV003407301RCV005887359RCV005887357RCV005887358RCV004814858RCV005887356RCV005887355
NM_006214.4(PHYH):c.610G>A (p.Gly204Ser) SNV
Germline		 Chr10:13288428 Likely pathogenic REFSUM DISEASE, ADULT, 1
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA118907 rs_104894173

3 SubmittersRCV000008025RCV003473055
NM_006214.4(PHYH):c.824G>A (p.Arg275Gln) SNV
Germline		 Chr10:13283694 Pathogenic/Likely pathogenic REFSUM DISEASE, ADULT, 1
Condition: not provided
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA118908 rs_104894174

4 SubmittersRCV000008026RCV001851728RCV003473056
NM_000288.4(PEX7):c.875T>A (p.Leu292Ter) SNV
Germline		 Chr6:136898213 Pathogenic Rhizomelic chondrodysplasia punctata type 1
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Condition: not provided
PEX7-related disorder
Peroxisome biogenesis disorder 9B
Phytanic acid storage disease
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Retinal disorder		 Criteria Provided
Multiple Submitters
No Conflicts
 CA340698 rs_1805137

30 SubmittersRCV000008222RCV000477898RCV000339271RCV000352824RCV000380952RCV005394139RCV006253453
NM_000288.4(PEX7):c.653C>T (p.Ala218Val) SNV
Germline		 Chr6:136869909 Pathogenic/Likely pathogenic Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Condition: not provided
Rhizomelic chondrodysplasia punctata
Phytanic acid storage disease
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
PEX7-related disorder		 Criteria Provided
Multiple Submitters
No Conflicts
 CA130482 rs_121909151

12 SubmittersRCV000008223RCV000032925RCV000656252RCV001831555RCV002504768RCV004732537
NM_000288.4(PEX7):c.340-10A>G SNV
Germline		 Chr6:136845605 Conflicting classifications of pathogenicity Peroxisome biogenesis disorder 9B
Phytanic acid storage disease
Rhizomelic chondrodysplasia punctata type 1
Condition: not provided
Retinal dystrophy
Inborn genetic diseases
Peroxisome biogenesis disorder
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B		 Criteria Provided
Conflicting Classifications
 CA119074 rs_267608255

13 SubmittersRCV000008229RCV000032116RCV000393497RCV000731239RCV004814859RCV005384640RCV005357095RCV005042014
NM_000288.4(PEX7):c.120C>G (p.Tyr40Ter) SNV
Germline		 Chr6:136822785 Pathogenic Peroxisome biogenesis disorder 9B
Rhizomelic chondrodysplasia punctata type 1
PEX7-related disorder
Phytanic acid storage disease
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Rhizomelic chondrodysplasia punctata
Inborn genetic diseases
Condition: not provided
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B		 Criteria Provided
Multiple Submitters
No Conflicts
 CA119075 rs_61753238

10 SubmittersRCV000008230RCV000147254RCV000324320RCV000763558RCV001826454RCV002512898RCV003137500RCV005031422
NM_000288.4(PEX7):c.-45C>T SNV
Unknown		 Chr6:136822621 Likely pathogenic Phytanic acid storage disease
Peroxisome biogenesis disorder 9B		 Criteria Provided
Single Submitter
 CA343127 rs_267608252

2 SubmittersRCV000032114RCV004566793
NM_000288.4(PEX7):c.188+1G>C SNV
Germline		 Chr6:136825272 Pathogenic/Likely pathogenic Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Phytanic acid storage disease
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA274207 rs_267608254

6 SubmittersRCV000169353RCV001068245RCV002485052RCV003233479
NM_006214.4(PHYH):c.678+5G>T SNV
Germline		 Chr10:13288355 Conflicting classifications of pathogenicity Condition: not provided
Retinitis pigmentosa
Phytanic acid storage disease
Retinal dystrophy
PHYH-related disorder
Phytanoyl-CoA hydroxylase deficiency
Colon adenocarcinoma
Thymoma
Sarcoma
Acute myeloid leukemia
not specified
Malignant tumor of esophagus
Nonpapillary renal cell carcinoma
Familial cancer of breast		 Criteria Provided
Conflicting Classifications
 CA246715 rs_201499815

13 SubmittersRCV000179461RCV000504947RCV000673770RCV001075452RCV003927682RCV005361081RCV005892024RCV005892029RCV005892028RCV005892025RCV006268652RCV005892026RCV005892027RCV005892023
NM_006214.4(PHYH):c.734G>A (p.Arg245Gln) SNV
Germline		 Chr10:13283784 Conflicting classifications of pathogenicity not specified
Phytanic acid storage disease
Nonsyndromic cleft lip palate
Condition: not provided
Vitamin D-dependent rickets type II with alopecia
Retinal dystrophy
Gastric cancer
Melanoma
Acute myeloid leukemia
Nonpapillary renal cell carcinoma
Adrenocortical carcinoma, hereditary		 Criteria Provided
Conflicting Classifications
 CA203488 rs_62619919

15 SubmittersRCV000179914RCV000665931RCV000755125RCV000950185RCV001258288RCV004816303RCV005892046RCV005892047RCV005892043RCV005892044RCV005892045
NM_006214.4(PHYH):c.606C>A (p.Asn202Lys) SNV
Germline		 Chr10:13288432 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided
Inborn genetic diseases
Retinal dystrophy		 Criteria Provided
Conflicting Classifications
 CA5412302 rs_201979258

5 SubmittersRCV000359852RCV000430932RCV002520543RCV004816526
NM_006214.4(PHYH):c.356C>T (p.Thr119Met) SNV
Germline		 Chr10:13294486 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided
PHYH-related disorder
Retinal dystrophy		 Criteria Provided
Conflicting Classifications
 CA5412402 rs_34571629

8 SubmittersRCV000319288RCV000960582RCV003930251RCV004816528
NM_006214.4(PHYH):c.76-9A>T SNV
Germline		 Chr10:13298254 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided
PHYH-related disorder		 Criteria Provided
Conflicting Classifications
 CA5412492 rs_368542152

3 SubmittersRCV000345853RCV001434964RCV003967857
NM_006214.4(PHYH):c.601C>G (p.Arg201Gly) SNV
Germline		 Chr10:13288437 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided
not specified		 Criteria Provided
Conflicting Classifications
 CA5412303 rs_143957922

7 SubmittersRCV000267540RCV000487565RCV006441486
NM_006214.4(PHYH):c.321G>T (p.Ser107=) SNV
Germline		 Chr10:13294521 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA10631235 rs_115198308

2 SubmittersRCV000373480RCV003765759
NM_006214.4(PHYH):c.792C>T (p.His264=) SNV
Germline		 Chr10:13283726 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided
PHYH-related disorder		 Criteria Provided
Conflicting Classifications
 CA5412241 rs_372047384

3 SubmittersRCV000399862RCV000913767RCV003977863
NM_000288.4(PEX7):c.277C>T (p.Gln93Ter) SNV
Germline		 Chr6:136826407 Pathogenic/Likely pathogenic Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Rhizomelic chondrodysplasia punctata
Connective tissue disorder
Phytanic acid storage disease
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B		 Criteria Provided
Multiple Submitters
No Conflicts
 CA4017545 rs_763514968

6 SubmittersRCV000409536RCV001387967RCV001828373RCV002278634RCV002502423
NM_000288.4(PEX7):c.695G>A (p.Arg232Gln) SNV
Germline		 Chr6:136869951 Conflicting classifications of pathogenicity Condition: not provided
Phytanic acid storage disease
Rhizomelic chondrodysplasia punctata type 1
Peroxisome biogenesis disorder 9B
Peroxisome biogenesis disorder 9B
Rhizomelic chondrodysplasia punctata type 1
PEX7-related disorder		 Criteria Provided
Conflicting Classifications
 CA4017697 rs_191969418

6 SubmittersRCV000591798RCV000765867RCV001081418RCV001151970RCV004732960
NM_006214.4(PHYH):c.414+2T>C SNV
Unknown		 Chr10:13294426 Likely pathogenic Phytanic acid storage disease No Assertion Criteria Provided
 CA376036819 rs_1554784939

1 SubmittersRCV000674886
NM_006214.4(PHYH):c.244C>G (p.Arg82Gly) SNV
Germline		 Chr10:13295497 Conflicting classifications of pathogenicity Nonsyndromic cleft lip palate
Condition: not provided
not specified
Phytanic acid storage disease		 Criteria Provided
Conflicting Classifications
 CA5412447 rs_145404396

7 SubmittersRCV000755126RCV001404622RCV001731916RCV003130029
NM_006214.4(PHYH):c.135-1G>C SNV
Germline		 Chr10:13295607 Pathogenic/Likely pathogenic Refsum syndrome
Condition: not provided
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA203283602 rs_1057272016

4 SubmittersRCV001003121RCV001862725RCV003473541
NM_006214.4(PHYH):c.497-2A>G SNV
Germline		 Chr10:13288543 Pathogenic/Likely pathogenic Condition: not provided
Retinal dystrophy
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA5412331 rs_144169488

5 SubmittersRCV001058049RCV001075231RCV001784612
NM_006214.4(PHYH):c.530A>G (p.Asp177Gly) SNV
Germline		 Chr10:13288508 Conflicting classifications of pathogenicity Retinal dystrophy
Condition: not provided
Phytanic acid storage disease		 Criteria Provided
Conflicting Classifications
 CA5412325 rs_770262329

7 SubmittersRCV001074765RCV001092476RCV003473705
NM_006214.4(PHYH):c.830C>A (p.Ala277Glu) SNV
Germline		 Chr10:13281109 Pathogenic/Likely pathogenic Condition: not provided
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA376051681 rs_1211539675

2 SubmittersRCV001092475RCV004761930
NM_006214.4(PHYH):c.948T>C (p.Asn316=) SNV
Germline		 Chr10:13280991 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA5412200 rs_143734330

2 SubmittersRCV001104174RCV001522937
NM_006214.4(PHYH):c.679G>T (p.Gly227Trp) SNV
Germline		 Chr10:13283839 Conflicting classifications of pathogenicity Phytanic acid storage disease
Condition: not provided
Inborn genetic diseases
Intellectual disability		 Criteria Provided
Conflicting Classifications
 CA5412260 rs_201936962

7 SubmittersRCV001106948RCV001699508RCV002555045RCV005626331
NM_006214.4(PHYH):c.497-1G>A SNV
Germline		 Chr10:13288542 Likely pathogenic Condition: not provided
Phytanic acid storage disease
Hepatocellular carcinoma		 Criteria Provided
Multiple Submitters
No Conflicts
 CA5412330 rs_761927136

3 SubmittersRCV001973508RCV003475265RCV005925434
NM_006214.4(PHYH):c.502A>T (p.Lys168Ter) SNV
Unknown		 Chr10:13288536 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 CA376035899 rs_1835618953

1 SubmittersRCV002308280
NM_006214.4(PHYH):c.640A>T (p.Lys214Ter) SNV
Unknown		 Chr10:13288398 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 CA376035262 rs_753115080

1 SubmittersRCV002309016
NM_006214.4(PHYH):c.675G>A (p.Trp225Ter) SNV
Germline		 Chr10:13288363 Pathogenic/Likely pathogenic Condition: not provided
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA376035134 rs_1835606884

3 SubmittersRCV002741112RCV004571232
NM_006214.4(PHYH):c.124C>T (p.Gln42Ter) SNV
Unknown		 Chr10:13298197 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 CA5412486 rs_759970314

1 SubmittersRCV003472442
NM_006214.4(PHYH):c.578G>A (p.Trp193Ter) SNV
Unknown		 Chr10:13288460 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 CA376035529 rs_1448778830

1 SubmittersRCV003472446
NM_006214.4(PHYH):c.415-1G>T SNV
Unknown		 Chr10:13291913 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 CA376036539 rs_1835721943

1 SubmittersRCV003472447
NM_006214.4(PHYH):c.343G>T (p.Glu115Ter) SNV
Unknown		 Chr10:13294499 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 CA376037035 rs_747271385

1 SubmittersRCV003472450
NM_006214.4(PHYH):c.399C>G (p.Tyr133Ter) SNV
Unknown		 Chr10:13294443 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 CA376036855 rs_1835789883

1 SubmittersRCV003472451
NM_006214.4(PHYH):c.134+1G>A SNV
Germline		 Chr10:13298186 Likely pathogenic Condition: not provided
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA376038079 rs_2538664377

3 SubmittersRCV003572169RCV004574126
NM_006214.4(PHYH):c.678+2T>C SNV
Germline		 Chr10:13288358 Likely pathogenic Condition: not provided
Phytanic acid storage disease		 Criteria Provided
Multiple Submitters
No Conflicts
 CA5412282 rs_769744387

2 SubmittersRCV003667152RCV004574177
NM_006214.4(PHYH):c.76-1G>A SNV
Unknown		 Chr10:13298246 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter
 rs_751766259

1 SubmittersRCV004574538
NM_006214.4(PHYH):c.7C>T (p.Gln3Ter) SNV
Germline		 Chr10:13300036 Likely pathogenic Phytanic acid storage disease Criteria Provided
Single Submitter

1 SubmittersRCV005033110