TLK2 — 303 ClinVar variants

All ClinVar germline TLK2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 139 flagged for review →

41 Pathogenic · 9 Pathogenic/Likely pathogenic · 41 Likely pathogenic · 8 Conflicting · 2 Benign · 38 Likely benign · 164 Uncertain significance

Full TLK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 139

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 6

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

Predicted LoF vs a conflicting call 2

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 107

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

Predictors split 23

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

All TLK2 variants

Pathogenic 41

  • p.Arg123Ter Multiple submitters intellectual disability, autosomal dominant 57
  • p.Arg262Ter Multiple submitters intellectual disability, autosomal dominant 57
  • p.Arg61Ter Multiple submitters intellectual disability, autosomal dominant 57
  • p.Arg697Ter Multiple submitters
  • p.Gln280fs Multiple submitters
  • c.1122-167A>G Single submitter intellectual disability, autosomal dominant 57
  • c.1187_1188+18del Single submitter intellectual disability, autosomal dominant 57
  • c.1189-2A>G Single submitter Inborn genetic diseases
  • c.1286+1G>A Single submitter intellectual disability, autosomal dominant 57
  • c.1369-2A>G Single submitter
  • c.154-1G>A Single submitter intellectual disability, autosomal dominant 57
  • c.2079+1G>A Single submitter intellectual disability, autosomal dominant 57
  • c.267+1G>A Single submitter intellectual disability, autosomal dominant 57
  • p.Ala467fs Single submitter Inborn genetic diseases
  • p.Ala583fs Single submitter Inborn genetic diseases
  • p.Arg246Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Arg286_Asp287insTer Single submitter Inborn genetic diseases
  • p.Asn222fs Single submitter
  • p.Asn528fs Single submitter
  • p.Asn638fs Single submitter TLK2-related disorder
  • p.Gln13fs Single submitter intellectual disability, autosomal dominant 57
  • p.Gln13Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Gln352fs Single submitter
  • p.Gln472fs Single submitter intellectual disability, autosomal dominant 57
  • p.Gln551Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Glu453Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Glu49fs Single submitter intellectual disability, autosomal dominant 57
  • p.Glu68Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Ile576fs Single submitter
  • p.Leu238fs Single submitter Inborn genetic diseases
  • p.Leu622fs Single submitter intellectual disability, autosomal dominant 57
  • p.Lys456Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Met341fs Single submitter
  • p.Ser26fs Single submitter
  • p.Ser289fs Single submitter intellectual disability, autosomal dominant 57
  • p.Ser330Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Ser637Ter Single submitter
  • p.Trp477Ter Single submitter
  • p.Trp643Ter Single submitter Inborn genetic diseases
  • c.1460+2T>G No assertion criteria intellectual disability, autosomal dominant 57
  • c.1720+1G>T No assertion criteria intellectual disability, autosomal dominant 57

Pathogenic/Likely pathogenic 9

  • c.1121+1G>A Multiple submitters intellectual disability, autosomal dominant 57
  • c.1550+1G>A Multiple submitters intellectual disability, autosomal dominant 57
  • p.Arg122Ter Multiple submitters intellectual disability, autosomal dominant 57
  • p.Arg546Trp Multiple submitters Inborn genetic diseases
  • p.Arg703Ter Multiple submitters TLK2-related disorder
  • p.His496Arg Multiple submitters TLK2-related disorder
  • p.Ser595Leu Multiple submitters intellectual disability, autosomal dominant 57
  • p.Tyr259Ter Multiple submitters intellectual disability, autosomal dominant 57
  • p.Asp529Gly Single submitter intellectual disability, autosomal dominant 57

Likely pathogenic 41

  • p.Arg11Ter Multiple submitters intellectual disability, autosomal dominant 57
  • p.Cys195Ter Multiple submitters TLK2-related disorder
  • p.Gln252Ter Multiple submitters TLK2-related disorder
  • p.Pro658Arg Multiple submitters TLK2-related disorder
  • c.1121+1G>C Single submitter intellectual disability, autosomal dominant 57
  • c.1121+2dup Single submitter
  • c.1188+1G>A Single submitter intellectual disability, autosomal dominant 57
  • c.1286+5G>A Single submitter Developmental disorder
  • c.628-2_628del Single submitter
  • p.Ala489Thr Single submitter intellectual disability, autosomal dominant 57
  • p.Arg109Gln Single submitter ⚠
  • p.Arg240fs Single submitter neurodevelopmental disorder
  • p.Arg332fs Single submitter intellectual disability, autosomal dominant 57
  • p.Arg363Trp Single submitter
  • p.Arg494Trp Single submitter intellectual disability, autosomal dominant 57
  • p.Arg546Pro Single submitter
  • p.Arg65fs Single submitter intellectual disability, autosomal dominant 57
  • p.Asp607Asn Single submitter intellectual disability, autosomal dominant 57 ⚠
  • p.Cys626Tyr Single submitter TLK2-related disorder
  • p.Gln126Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Gln200fs Single submitter
  • p.Gln209Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Gln383Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Glu138Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Glu542Ter Single submitter intellectual disability, autosomal dominant 57
  • p.Gly593Asp Single submitter
  • p.Gly608Ala Single submitter
  • p.His471Arg Single submitter intellectual disability, autosomal dominant 57
  • p.Leu131Ter Single submitter TLK2-related disorder
  • p.Leu296Pro Single submitter neurodevelopmental disorder
  • p.Leu342Ser Single submitter syndromic microphthalmia
  • p.Leu530Pro Single submitter intellectual disability, autosomal dominant 57
  • p.Ser196fs Single submitter intellectual disability, autosomal dominant 57
  • p.Ser278Pro Single submitter
  • p.Ser595Pro Single submitter intellectual disability, autosomal dominant 57
  • p.Thr161fs Single submitter
  • p.Trp620Ter Single submitter
  • p.Tyr650Cys Single submitter TLK2-related disorder
  • p.Tyr718Cys Single submitter
  • p.Glu333Ter No assertion criteria Rare genetic intellectual disability
  • p.Gly527Arg No assertion criteria intellectual disability, autosomal dominant 57

Conflicting classifications of pathogenicity 8

  • p.Arg339Gln Single submitter intellectual disability, autosomal dominant 57 ⚠
  • p.Arg339Trp Single submitter intellectual disability, autosomal dominant 57 ⚠
  • p.Arg546Gln Single submitter intellectual disability, autosomal dominant 57 ⚠
  • p.Arg698Ter Single submitter intellectual disability, autosomal dominant 57 ⚠
  • p.Arg724Ter Single submitter intellectual disability, autosomal dominant 57 ⚠
  • p.Gly297Asp Single submitter TLK2-related disorder ⚠
  • p.Ile587Arg Single submitter Inborn genetic diseases ⚠
  • p.Ser517Leu Single submitter intellectual disability, autosomal dominant 57 ⚠

Benign 2

  • p.Pro624= Multiple submitters intellectual disability, autosomal dominant 57
  • c.1551-58G>A Single submitter Inborn genetic diseases

Likely benign 38

Uncertain significance 164