KLHL20 — 80 ClinVar variants

All ClinVar germline KLHL20 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 67 flagged for review →

4 Pathogenic · 1 Pathogenic/Likely pathogenic · 2 Likely pathogenic · 1 Conflicting · 2 Benign · 4 Likely benign · 66 Uncertain significance

Full KLHL20 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 67

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 agree, ClinVar conflicts 1

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

KLHL20 p.Gly324Asp Conflicting Single submitter

Predictors lean, ClinVar uncertain 48

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

Predictors split 18

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

KLHL20 p.Arg105His Uncertain significance Single submitter
KLHL20 p.Arg315Pro Benign Single submitter
KLHL20 p.Asn485Ser Uncertain significance Single submitter
KLHL20 p.Glu116Lys Uncertain significance Single submitter
KLHL20 p.Gly586Arg Uncertain significance Single submitter
KLHL20 p.Ile571Thr Uncertain significance Single submitter
KLHL20 p.Met236Ile Uncertain significance Single submitter
KLHL20 p.Met493Val Uncertain significance Single submitter
KLHL20 p.Phe414Leu Uncertain significance Single submitter
KLHL20 p.Ser468Phe Uncertain significance Single submitter
KLHL20 p.Thr404Arg Uncertain significance Single submitter
KLHL20 p.Tyr567Asp Uncertain significance Single submitter
KLHL20 p.Val360Ile Uncertain significance Single submitter
KLHL20 p.Val477Ala Uncertain significance Single submitter
KLHL20 p.Gln421Arg Pathogenic No assertion criteria
neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities
KLHL20 p.Gly546Arg Pathogenic No assertion criteria
neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities
KLHL20 p.Gly593Trp Pathogenic No assertion criteria
neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities
KLHL20 p.Ser405Asn Pathogenic No assertion criteria
neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities

All KLHL20 variants

Pathogenic 4

p.Gln421Arg No assertion criteria neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities ⚠
p.Gly546Arg No assertion criteria neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities ⚠
p.Gly593Trp No assertion criteria neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities ⚠
p.Ser405Asn No assertion criteria neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities ⚠

Pathogenic/Likely pathogenic 1

p.Gly357Arg Multiple submitters Seizure

Likely pathogenic 2

p.Gly407Arg Single submitter
p.Pro210Arg Single submitter Global developmental delay

Conflicting classifications of pathogenicity 1

p.Gly324Asp Single submitter ⚠

Benign 2

c.756+8T>C Single submitter
p.Arg315Pro Single submitter ⚠

Likely benign 4

c.1430-8C>T Single submitter
p.Arg8= Single submitter
p.Asp178= Single submitter
p.Asp507Glu Single submitter neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities

Uncertain significance 66

p.Ala81Gly Single submitter ⚠
p.Arg105His Single submitter ⚠
p.Arg112Gln Single submitter ⚠
p.Arg13Leu Single submitter ⚠
p.Arg442Trp Single submitter ⚠
p.Arg486Gly Single submitter ⚠
p.Arg544_Ser545delinsGlyIle Single submitter
p.Arg65Gln Single submitter ⚠
p.Arg83Leu Single submitter neurodevelopmental disorder ⚠
p.Asn438Ser Single submitter ⚠
p.Asn485Ser Single submitter ⚠
p.Asn553Ser Single submitter ⚠
p.Asp516Val Single submitter ⚠
p.Cys356Arg Single submitter KLHL20-related disorder ⚠
p.Cys9Phe Single submitter ⚠
p.Cys9Tyr Single submitter ⚠
p.Gln194Glu Single submitter ⚠
p.Gln249Lys Single submitter ⚠
p.Glu116Gln Single submitter ⚠
p.Glu116Lys Single submitter ⚠
p.Glu16Ala Single submitter ⚠
p.Glu202Gly Single submitter ⚠
p.Gly325Asp Single submitter ⚠
p.Gly325Ser Single submitter ⚠
p.Gly452Asp Single submitter ⚠
p.Gly459Glu Single submitter
p.Gly586Arg Single submitter ⚠
p.Ile217Val Single submitter ⚠
p.Ile46Val Single submitter ⚠
p.Ile490Val Single submitter ⚠
p.Ile571Thr Single submitter ⚠
p.Ile79Val Single submitter ⚠
p.Leu367Ser Single submitter ⚠
p.Leu411Val Single submitter ⚠
p.Leu427Phe Single submitter ⚠
p.Lys240Ter Single submitter
p.Met236Ile Single submitter ⚠
p.Met493Val Single submitter ⚠
p.Met601Val Single submitter ⚠
p.Phe414Leu Single submitter ⚠
p.Phe574Ser Single submitter ⚠
p.Pro167Leu Single submitter ⚠
p.Pro297Leu Single submitter ⚠
p.Pro398Leu Single submitter ⚠
p.Pro435Leu Single submitter ⚠
p.Pro529Ser Single submitter ⚠
p.Ser219Phe Single submitter ⚠
p.Ser263Thr Single submitter ⚠
p.Ser381Gly Single submitter neurodevelopmental disorder with early-onset seizures, facial dysmorphism, and behavioral abnormalities ⚠
p.Ser447Asn Single submitter ⚠
p.Ser468Phe Single submitter ⚠
p.Thr107Ala Single submitter ⚠
p.Thr404Arg Single submitter ⚠
p.Thr448Ile Single submitter ⚠
p.Thr518Ala Single submitter ⚠
p.Trp326Cys Single submitter KLHL20-related disorder ⚠
p.Trp609Leu Single submitter ⚠
p.Tyr416fs Single submitter
p.Tyr567Asp Single submitter ⚠
p.Val21Ile Single submitter ⚠
p.Val360Ile Single submitter ⚠
p.Val410Gly Single submitter ⚠
p.Val430Ile Single submitter ⚠
p.Val477Ala Single submitter ⚠
p.Asn485Lys No assertion criteria ⚠
p.Leu86fs No assertion criteria prostate cancer