RPS6KA3 — 559 ClinVar variants

All ClinVar germline RPS6KA3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 138 flagged for review →

102 Pathogenic · 6 Pathogenic/Likely pathogenic · 64 Likely pathogenic · 16 Conflicting · 51 Benign · 21 Benign/Likely benign · 142 Likely benign · 157 Uncertain significance

Full RPS6KA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 138

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 1

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

Predictors agree, ClinVar conflicts 7

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

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 102

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 27

The independent predictors disagree with each other — read with care.

All RPS6KA3 variants

Pathogenic 102

Pathogenic/Likely pathogenic 6

  • c.1603-5A>G Multiple submitters Coffin-Lowry syndrome
  • c.632-1G>C Multiple submitters Inborn genetic diseases
  • p.Arg729Gln Multiple submitters Inborn genetic diseases
  • p.Arg729Trp Multiple submitters Coffin-Lowry syndrome
  • p.Leu298fs Multiple submitters RPS6KA3-related disorder
  • p.Leu71Ter Multiple submitters Coffin-Lowry syndrome

Likely pathogenic 64

Conflicting classifications of pathogenicity 16

Benign 51

Benign/Likely benign 21

  • c.1000-10del Multiple submitters Coffin-Lowry syndrome
  • c.1353+5A>T Multiple submitters intellectual disability, X-linked 19
  • c.244-5T>C Multiple submitters Inborn genetic diseases
  • c.406+12C>A Multiple submitters Coffin-Lowry syndrome
  • c.631+12del Multiple submitters Coffin-Lowry syndrome
  • c.631+12dup Multiple submitters Coffin-Lowry syndrome
  • c.631+18G>A Multiple submitters Coffin-Lowry syndrome
  • p.Ala570= Multiple submitters intellectual disability, X-linked 19
  • p.Arg723His Multiple submitters Inborn genetic diseases
  • p.Asn414= Multiple submitters Inborn genetic diseases
  • p.Asp663= Multiple submitters Inborn genetic diseases
  • p.Glu360= Multiple submitters intellectual disability, X-linked 19
  • p.Glu628Asp Multiple submitters intellectual disability, X-linked 19
  • p.His341= Multiple submitters intellectual disability, X-linked 19
  • p.Ile407Val Multiple submitters Inborn genetic diseases
  • p.Ile416Val Multiple submitters intellectual disability, X-linked 19
  • p.Ile47Val Multiple submitters intellectual disability, X-linked 19
  • p.Leu71= Multiple submitters Inborn genetic diseases
  • p.Ser432= Multiple submitters intellectual disability, X-linked 19
  • p.Thr362= Multiple submitters intellectual disability, X-linked 19
  • p.Val404= Multiple submitters Inborn genetic diseases

Likely benign 142

  • c.1354-17A>C Multiple submitters intellectual disability, X-linked 19
  • c.1444-5T>C Multiple submitters
  • c.244-17C>T Multiple submitters Coffin-Lowry syndrome
  • c.325+16A>G Multiple submitters Coffin-Lowry syndrome
  • c.406+14G>A Multiple submitters Coffin-Lowry syndrome
  • c.775-17A>G Multiple submitters intellectual disability, X-linked 19
  • c.845+108A>C Multiple submitters
  • p.Ala695= Multiple submitters intellectual disability, X-linked 19
  • p.Asp650= Multiple submitters
  • p.Glu320= Multiple submitters
  • c.1000-10T>C Single submitter Coffin-Lowry syndrome
  • c.1000-15T>A Single submitter intellectual disability, X-linked 19
  • c.1000-18T>C Single submitter intellectual disability, X-linked 19
  • c.1000-18T>G Single submitter intellectual disability, X-linked 19
  • c.1000-7C>T Single submitter intellectual disability, X-linked 19
  • c.1000-8C>T Single submitter intellectual disability, X-linked 19
  • c.1103-11A>G Single submitter intellectual disability, X-linked 19
  • c.1103-14C>G Single submitter intellectual disability, X-linked 19
  • c.1227+124G>A Single submitter
  • c.1227+14T>C Single submitter Coffin-Lowry syndrome
  • c.1227+18T>C Single submitter intellectual disability, X-linked 19
  • c.1227+7G>A Single submitter intellectual disability, X-linked 19
  • c.1228-563G>C Single submitter
  • c.126+19C>T Single submitter Coffin-Lowry syndrome
  • c.127-15C>T Single submitter
  • c.127-19C>G Single submitter intellectual disability, X-linked 19
  • c.127-9440G>A Single submitter
  • c.1353+11T>C Single submitter intellectual disability, X-linked 19
  • c.1354-15A>G Single submitter intellectual disability, X-linked 19
  • c.1443+19A>G Single submitter intellectual disability, X-linked 19
  • c.1443+9del Single submitter intellectual disability, X-linked 19
  • c.1444-4A>T Single submitter
  • c.1602+13A>C Single submitter intellectual disability, X-linked 19
  • c.1602+17C>T Single submitter intellectual disability, X-linked 19
  • c.1603-19T>G Single submitter intellectual disability, X-linked 19
  • c.1765-10C>T Single submitter intellectual disability, X-linked 19
  • c.1841+16A>G Single submitter intellectual disability, X-linked 19
  • c.1841+261AC[3] Single submitter
  • c.1842-20T>C Single submitter intellectual disability, X-linked 19
  • c.1842-300C>T Single submitter
  • c.1959+17A>C Single submitter intellectual disability, X-linked 19
  • c.1959+18T>C Single submitter intellectual disability, X-linked 19
  • c.1960-16A>T Single submitter Coffin-Lowry syndrome
  • c.1960-7A>G Single submitter intellectual disability, X-linked 19
  • c.2100+15A>G Single submitter intellectual disability, X-linked 19
  • c.2100+18G>T Single submitter intellectual disability, X-linked 19
  • c.2100+217G>A Single submitter
  • c.2101-19C>A Single submitter intellectual disability, X-linked 19
  • c.2101-19C>T Single submitter
  • c.243+17T>C Single submitter
  • c.243+19C>T Single submitter Coffin-Lowry syndrome
  • c.244-11C>T Single submitter intellectual disability, X-linked 19
  • c.244-201A>C Single submitter
  • c.244-20T>C Single submitter intellectual disability, X-linked 19
  • c.244-4G>T Single submitter intellectual disability, X-linked 19
  • c.244-7A>C Single submitter intellectual disability, X-linked 19
  • c.325+197C>T Single submitter
  • c.326-20A>C Single submitter intellectual disability, X-linked 19
  • c.406+11G>A Single submitter intellectual disability, X-linked 19
  • c.486+20T>G Single submitter intellectual disability, X-linked 19
  • c.593+11A>G Single submitter intellectual disability, X-linked 19
  • c.593+332C>T Single submitter
  • c.593+7A>C Single submitter intellectual disability, X-linked 19
  • c.594-15C>A Single submitter intellectual disability, X-linked 19
  • c.594-18T>C Single submitter intellectual disability, X-linked 19
  • c.631+17C>T Single submitter intellectual disability, X-linked 19
  • c.631+20T>C Single submitter intellectual disability, X-linked 19
  • c.631+7A>G Single submitter
  • c.631+9A>C Single submitter Coffin-Lowry syndrome
  • c.632-248G>A Single submitter
  • c.70-15C>T Single submitter intellectual disability, X-linked 19
  • c.70-19C>A Single submitter Coffin-Lowry syndrome
  • c.774+12A>C Single submitter intellectual disability, X-linked 19
  • c.775-184C>T Single submitter
  • c.775-207dup Single submitter
  • c.775-244dup Single submitter
  • c.775-65del Single submitter
  • c.846-13A>G Single submitter intellectual disability, X-linked 19
  • c.934+14_934+17del Single submitter intellectual disability, X-linked 19
  • c.934+14C>A Single submitter intellectual disability, X-linked 19
  • c.935-108ATTA[6] Single submitter
  • c.935-155C>T Single submitter
  • c.935-216G>A Single submitter
  • c.935-4A>T Single submitter intellectual disability, X-linked 19
  • c.999+18A>G Single submitter intellectual disability, X-linked 19
  • p.Ala443= Single submitter
  • p.Arg723Cys Single submitter Inborn genetic diseases
  • p.Asp459= Single submitter intellectual disability, X-linked 19
  • p.Gln95= Single submitter
  • p.Gly255= Single submitter intellectual disability, X-linked 19
  • p.Gly471= Single submitter intellectual disability, X-linked 19
  • p.Gly731= Single submitter
  • p.Ile545= Single submitter
  • p.Ile545Met Single submitter
  • p.Ile679= Single submitter intellectual disability, X-linked 19
  • p.Ile735= Single submitter Coffin-Lowry syndrome
  • p.Leu194= Single submitter Inborn genetic diseases
  • p.Leu257= Single submitter Coffin-Lowry syndrome
  • p.Leu298= Single submitter Inborn genetic diseases
  • p.Leu335= Single submitter intellectual disability, X-linked 19
  • p.Leu381= Single submitter Inborn genetic diseases
  • p.Leu640= Single submitter Coffin-Lowry syndrome
  • p.Lys132= Single submitter intellectual disability, X-linked 19
  • p.Phe129= Single submitter Coffin-Lowry syndrome
  • p.Pro293Ala Single submitter intellectual disability, X-linked 19
  • p.Pro346= Single submitter Coffin-Lowry syndrome
  • p.Pro373= Single submitter
  • p.Pro460= Single submitter Inborn genetic diseases
  • p.Pro474= Single submitter intellectual disability, X-linked 19
  • p.Pro617= Single submitter intellectual disability, X-linked 19
  • p.Ser635= Single submitter intellectual disability, X-linked 19
  • p.Thr106= Single submitter intellectual disability, X-linked 19
  • p.Thr354= Single submitter intellectual disability, X-linked 19
  • p.Thr706= Single submitter intellectual disability, X-linked 19
  • p.Val101= Single submitter intellectual disability, X-linked 19
  • p.Val109= Single submitter Coffin-Lowry syndrome
  • p.Val489= Single submitter Coffin-Lowry syndrome
  • p.Val548= Single submitter intellectual disability, X-linked 19
  • c.1000-11_1000-10del No assertion criteria RPS6KA3-related disorder
  • c.1227+9A>G No assertion criteria RPS6KA3-related disorder
  • c.326-12A>G No assertion criteria RPS6KA3-related disorder
  • c.631+9_631+12del No assertion criteria RPS6KA3-related disorder
  • c.845+8del No assertion criteria RPS6KA3-related disorder
  • c.934+9T>G No assertion criteria RPS6KA3-related disorder
  • c.-4G>A No assertion criteria RPS6KA3-related disorder
  • c.-9G>A No assertion criteria RPS6KA3-related disorder
  • p.Ala175= No assertion criteria RPS6KA3-related disorder
  • p.Ala63= No assertion criteria RPS6KA3-related disorder
  • p.Asp120= No assertion criteria RPS6KA3-related disorder
  • p.Cys439= No assertion criteria RPS6KA3-related disorder
  • p.Glu37= No assertion criteria RPS6KA3-related disorder
  • p.Glu447= No assertion criteria RPS6KA3-related disorder
  • p.Ile440= No assertion criteria RPS6KA3-related disorder
  • p.Ile88= No assertion criteria RPS6KA3-related disorder
  • p.Leu107= No assertion criteria RPS6KA3-related disorder
  • p.Leu540= No assertion criteria RPS6KA3-related disorder
  • p.Leu655= No assertion criteria RPS6KA3-related disorder
  • p.Lys425= No assertion criteria RPS6KA3-related disorder
  • p.Lys437= No assertion criteria RPS6KA3-related disorder
  • p.Lys497= No assertion criteria RPS6KA3-related disorder
  • p.Thr210= No assertion criteria RPS6KA3-related disorder
  • p.Val239= No assertion criteria RPS6KA3-related disorder

Uncertain significance 157