ACAN — 1679 ClinVar variants

All ClinVar germline ACAN variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 906 flagged for review →

125 Pathogenic · 8 Pathogenic/Likely pathogenic · 70 Likely pathogenic · 44 Conflicting · 118 Benign · 39 Benign/Likely benign · 369 Likely benign · 906 Uncertain significance

Full ACAN gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 906

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors vs ClinVar 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 445

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 445

Predictors split 438

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 438

All ACAN variants

Pathogenic 125

Pathogenic/Likely pathogenic 8

  • c.7302+1G>A Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Arg386Ter Multiple submitters
  • p.Arg675Ter Multiple submitters spondyloepiphyseal dysplasia, Kimberley type
  • p.Cys2304Ter Multiple submitters ACAN-related disorder
  • p.Thr259fs Multiple submitters
  • p.Trp377Ter Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Tyr517Ter Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Glu1847Ter No assertion criteria

Likely pathogenic 70

  • c.1733-2A>G Multiple submitters spondyloepiphyseal dysplasia, Kimberley type
  • p.Asp2419Asn Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • c.1051+1G>A Single submitter
  • c.1429+1G>T Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • c.1732+1G>T Single submitter
  • c.1733-1G>C Single submitter
  • c.2266+1G>T Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • c.455-3_457del Single submitter
  • c.630-2A>C Single submitter
  • c.6946+1G>T Single submitter spondyloepiphyseal dysplasia
  • c.757+1G>A Single submitter ACAN-related disorder
  • c.757+2T>C Single submitter
  • c.758-1G>A Single submitter
  • p.Ala2277fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Ala863fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Arg173fs Single submitter ACAN-related disorder
  • p.Asp206delinsGlyTer Single submitter osteochondritis dissecans
  • p.Asp953fs Single submitter spondyloepiphyseal dysplasia, Kimberley type
  • p.Cys2331Ter Single submitter spondyloepiphyseal dysplasia, Kimberley type
  • p.Gln1778Ter Single submitter
  • p.Gln514Ter Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Glu1447Ter Single submitter ACAN-related short stature spectrum
  • p.Glu1953fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Glu2221Ter Single submitter
  • p.Glu2383Ter Single submitter
  • p.Glu406fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Glu83Ter Single submitter spondyloepimetaphyseal dysplasia, aggrecan type
  • p.Gly554fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Gly578Arg Single submitter
  • p.Gly625fs Single submitter
  • p.Gly756Arg Single submitter ⚠
  • p.Gly921_Asp922insTer Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.His2460fs Single submitter
  • p.Ile398fs Single submitter
  • p.Ile701fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Ile729_Leu730insTer Single submitter
  • p.Leu302Pro Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Leu513fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Pro846fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Ser1611fs Single submitter
  • p.Ser1740Ter Single submitter Autosomal dominant ACAN-related disorders
  • p.Ser540fs Single submitter Autosomal dominant ACAN-related disorders
  • p.Ser776fs Single submitter
  • p.Ser802fs Single submitter
  • p.Ser845Ter Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Ser883fs Single submitter
  • p.Ser98fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Thr45fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Trp443Ter Single submitter
  • p.Trp75fs Single submitter osteochondritis dissecans
  • p.Trp928Ter Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Tyr109Asn Single submitter
  • p.Tyr1922Ter Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Val1476fs Single submitter short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • c.6833-1G>A No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • c.-7-2A>T No assertion criteria osteochondritis dissecans
  • p.Ala2280fs No assertion criteria ACAN-related disorder
  • p.Ala583fs No assertion criteria spondyloepiphyseal dysplasia, Kimberley type
  • p.Asp2078fs No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Gln373_Thr374insTer No assertion criteria osteochondritis dissecans
  • p.Gln464Ter No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Glu2267Ter No assertion criteria Short stature
  • p.Gly2416Asp No assertion criteria ACAN-related disorder
  • p.Lys2479fs No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Lys313fs No assertion criteria ACAN-related disorder
  • p.Met1Thr No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Phe1629fs No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Phe2448fs No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Pro1610fs No assertion criteria osteochondritis dissecans
  • p.Pro2064fs No assertion criteria short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans

Conflicting classifications of pathogenicity 44

Benign 118

Benign/Likely benign 39

  • c.1051+10G>A Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • c.1430-5C>T Multiple submitters
  • c.70+9A>T Multiple submitters
  • p.Ala1213Thr Multiple submitters spondyloepimetaphyseal dysplasia, aggrecan type
  • p.Ala613= Multiple submitters
  • p.Arg2376= Multiple submitters
  • p.Arg530Gln Multiple submitters Inborn genetic diseases
  • p.Arg617His Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Arg668Gln Multiple submitters ⚠
  • p.Asn2408= Multiple submitters
  • p.Asp102Glu Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Asp1390Glu Multiple submitters spondyloepiphyseal dysplasia, Kimberley type ⚠
  • p.Asp194= Multiple submitters
  • p.Asp2411Glu Multiple submitters spondyloepimetaphyseal dysplasia, aggrecan type ⚠
  • p.Cys2485= Multiple submitters
  • p.Cys643= Multiple submitters
  • p.Gln2538Arg Multiple submitters osteochondritis dissecans
  • p.Gly1849Val Multiple submitters
  • p.Gly2000Ser Multiple submitters
  • p.Gly395Ser Multiple submitters
  • p.Leu146= Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Leu1855Phe Multiple submitters
  • p.Phe456Leu Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans ⚠
  • p.Pro2058Leu Multiple submitters
  • p.Pro414= Multiple submitters
  • p.Pro56= Multiple submitters
  • p.Pro864Leu Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Pro913Thr Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Ser1449= Multiple submitters
  • p.Ser2120Arg Multiple submitters ⚠
  • p.Ser2508= Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Ser490Leu Multiple submitters spondyloepimetaphyseal dysplasia, aggrecan type
  • p.Ser850Gly Multiple submitters
  • p.Thr1403Ala Multiple submitters osteochondritis dissecans
  • p.Thr1622Ala Multiple submitters
  • p.Thr371= Multiple submitters
  • p.Thr62= Multiple submitters spondyloepiphyseal dysplasia, Kimberley type
  • p.Tyr2003= Multiple submitters short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans
  • p.Val749= Multiple submitters spondyloepimetaphyseal dysplasia, aggrecan type

Likely benign 369

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 906

Showing the top 300 by review status; the full set is in the sitemap.