Pseudoxanthoma elasticum: genes and variants
Explore variant evidence for Pseudoxanthoma elasticum across 1 analyzed protein (ABCC6). Linked ClinVar records include 67 pathogenic or likely pathogenic variants, 251 variants of uncertain significance and 43 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Source labels are pooled across this disease family.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Pseudoxanthoma elasticum
ABCC6: ATP-binding cassette sub-family C member 6
Its ATP-dependent transport activity in liver and other tissues is required indirectly for maintaining extracellular pyrophosphate, a major inhibitor of inappropriate mineralization. Loss-of-function variants cause pseudoxanthoma elasticum and can promote calcification of skin, retina, and arteries.
67 ClinVar pathogenic / likely pathogenic and 294 uncertain variants in ABCC6 have source records linked to Pseudoxanthoma elasticum. Association strength is not clinical gene validity.
Where Pseudoxanthoma elasticum variants cluster
- ABCC6 Cytoplasmic (positions 1105–1175): 11 of 67 ClinVar pathogenic / likely pathogenic variants, 3.5× more than its size predicts.
- ABCC6 Cytoplasmic (positions 1220–1503): 25 of 67 ClinVar pathogenic / likely pathogenic variants, 2.0× more than its size predicts.
- ABCC6 ABC transporter 1 (positions 629–853): 17 of 67 ClinVar pathogenic / likely pathogenic variants, 1.7× more than its size predicts.
- ABCC6 Cytoplasmic (positions 371–426): 4 of 67 ClinVar pathogenic / likely pathogenic variants, 1.6× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Pseudoxanthoma elasticum
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| ABCC6 R760Q | 760 | ABC transporter 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1114P | 1114 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1114C | 1114 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1114H | 1114 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1138Q | 1138 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1138W | 1138 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 G1133A | 1133 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R419Q | 419 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R600C | 600 | Cytoplasmic | Pathogenic / likely pathogenic (★★) |
| ABCC6 R760W | 760 | ABC transporter 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R807W | 807 | ABC transporter 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R807Q | 807 | ABC transporter 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 T811M | 811 | ABC transporter 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 T1130M | 1130 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1221H | 1221 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1221C | 1221 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 G1296D | 1296 | ABC transporter 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 T1301I | 1301 | ABC transporter 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 G1302R | 1302 | ABC transporter 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1339H | 1339 | ABC transporter 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R419W | 419 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R487Q | 487 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1339C | 1339 | ABC transporter 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R518Q | 518 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 G755R | 755 | ABC transporter 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R765Q | 765 | ABC transporter 1 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1235W | 1235 | Cytoplasmic | Pathogenic / likely pathogenic (★★) |
| ABCC6 E1245D | 1245 | Cytoplasmic | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1314W | 1314 | ABC transporter 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 R1164Q | 1164 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 E1400K | 1400 | ABC transporter 2 | Pathogenic / likely pathogenic (★★) |
| ABCC6 V1298F | 1298 | ABC transporter 2 | Pathogenic / likely pathogenic (★) |
| ABCC6 Q1347H | 1347 | ABC transporter 2 | Pathogenic / likely pathogenic (★) |
| ABCC6 R1138P | 1138 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★) |
| ABCC6 G1321S | 1321 | ABC transporter 2 | Pathogenic / likely pathogenic (★) |
| ABCC6 G666W | 666 | ABC transporter 1 | Pathogenic / likely pathogenic (★) |
| ABCC6 L726P | 726 | ABC transporter 1 | Pathogenic / likely pathogenic (★) |
| ABCC6 S1121W | 1121 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★) |
| ABCC6 G1200S | 1200 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic (★) |
| ABCC6 V787F | 787 | ABC transporter 1 | Pathogenic / likely pathogenic (★) |
| ABCC6 G1501S | 1501 | Cytoplasmic | Pathogenic / likely pathogenic (★) |
| ABCC6 G1133C | 1133 | ABC transmembrane type-1 2 | Pathogenic / likely pathogenic |
| ABCC6 L1335Q | 1335 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 S398G | 398 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic |
| ABCC6 T811R | 811 | ABC transporter 1 | Pathogenic / likely pathogenic |
| ABCC6 L1335P | 1335 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 G1354R | 1354 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 S1403R | 1403 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 G1405S | 1405 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 G663C | 663 | ABC transporter 1 | Pathogenic / likely pathogenic |
| ABCC6 G1299S | 1299 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 L355R | 355 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic |
| ABCC6 S398R | 398 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic |
| ABCC6 A594V | 594 | Transmembrane | Pathogenic / likely pathogenic |
| ABCC6 S1307P | 1307 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 Q1406K | 1406 | ABC transporter 2 | Pathogenic / likely pathogenic |
| ABCC6 W218C | 218 | Cytoplasmic | Pathogenic / likely pathogenic |
| ABCC6 G226R | 226 | Cytoplasmic | Pathogenic / likely pathogenic |
| ABCC6 S317R | 317 | ABC transmembrane type-1 1 | Pathogenic / likely pathogenic |
| ABCC6 L677P | 677 | ABC transporter 1 | Pathogenic / likely pathogenic |
Showing 60 of 67.
Uncertain variants prioritized for review in Pseudoxanthoma elasticum
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| ABCC6 G663S | 663 | ABC transporter 1 | Uncertain (★★) | +7: 2 other pathogenic changes within 3 positions; G663C at the same position is pathogenic; seen in 6.8e-06 of gnomAD DNA copies; REVEL 0.945 |
| ABCC6 S1403I | 1403 | ABC transporter 2 | Uncertain (★) | +7: 4 other pathogenic changes within 3 positions; S1403R at the same position is pathogenic; seen in 6.9e-07 of gnomAD DNA copies; REVEL 0.916 |
| ABCC6 G1321D | 1321 | ABC transporter 2 | Uncertain (★) | +7: 2 other pathogenic changes within 3 positions; G1321S at the same position is pathogenic; seen in 0 of gnomAD DNA copies; REVEL 0.946 |
| ABCC6 R1339L | 1339 | ABC transporter 2 | Uncertain | +7: 2 other pathogenic changes within 3 positions; R1339H at the same position is pathogenic; seen in 6.9e-07 of gnomAD DNA copies; REVEL 0.837 |
| ABCC6 Q1406H | 1406 | ABC transporter 2 | Conflicting reports (★) | +6: 3 other pathogenic changes within 3 positions; Q1406K at the same position is pathogenic; REVEL 0.875 |
| ABCC6 R807G | 807 | ABC transporter 1 | Uncertain | +6: 2 other pathogenic changes within 3 positions; R807W at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.74 |
Which prediction tools work for Pseudoxanthoma elasticum
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- REVEL: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CATVariant: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CADD: 96 out of 100
- PolyPhen-2: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 94 out of 100
- phyloP: 90 out of 100
Diseases related to Pseudoxanthoma elasticum
- Arterial calcification, generalized, of infancy, 2, also linked to ABCC6
- Pseudoxanthoma elasticum, forme fruste, also linked to ABCC6
- Optic atrophy, also linked to ABCC6
Frequently asked questions
Which genes have records linked to Pseudoxanthoma elasticum?
This view contains 1 analyzed proteins: ABCC6. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 67 pathogenic or likely pathogenic variants, 251 variants of uncertain significance and 43 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 6 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 408 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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