HAVCR2 — 92 ClinVar variants
All ClinVar germline HAVCR2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 45 flagged for review →
5 Conflicting · 3 Benign · 4 Benign/Likely benign · 32 Likely benign · 48 Uncertain significance
Full HAVCR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 45
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 3
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
- HAVCR2 p.Arg259His Conflicting Single submitter
- HAVCR2 p.Ile117Leu Conflicting Single submitter
-
HAVCR2 p.Thr101Ile
Conflicting
Single submitter
subcutaneous panniculitis-like T-cell lymphoma
Predictors lean, ClinVar uncertain 35
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- HAVCR2 p.Asp170Val Uncertain significance Multiple submitters
- HAVCR2 p.Gln175Arg Uncertain significance Multiple submitters
- HAVCR2 p.Ala147Gly Uncertain significance Single submitter
- HAVCR2 p.Ala43Pro Uncertain significance Single submitter
- HAVCR2 p.Arg140Trp Uncertain significance Single submitter
- HAVCR2 p.Arg150Gly Uncertain significance Single submitter
- HAVCR2 p.Arg259Cys Uncertain significance Single submitter
- HAVCR2 p.Asn172Lys Uncertain significance Single submitter
- HAVCR2 p.Asn172Ser Uncertain significance Single submitter
- HAVCR2 p.Asn190Asp Uncertain significance Single submitter
- HAVCR2 p.Asn278Ile Uncertain significance Single submitter
- HAVCR2 p.Asn278Ser Uncertain significance Single submitter
- HAVCR2 p.Asn85Ser Uncertain significance Single submitter
- HAVCR2 p.Asp194Gly Uncertain significance Single submitter
- HAVCR2 p.Asp71Asn Uncertain significance Single submitter
- HAVCR2 p.Asp74Glu Uncertain significance Single submitter
- HAVCR2 p.Cys282Gly Uncertain significance Single submitter
- HAVCR2 p.Glu182Lys Uncertain significance Single submitter
- HAVCR2 p.Gly64Ser Uncertain significance Single submitter
- HAVCR2 p.His157Arg Uncertain significance Single submitter
- HAVCR2 p.Ile129Val Uncertain significance Single submitter
- HAVCR2 p.Ile205Thr Uncertain significance Single submitter
- HAVCR2 p.Ile267Val Uncertain significance Single submitter
- HAVCR2 p.Ile97Thr Uncertain significance Single submitter
- HAVCR2 p.Lys55Glu Uncertain significance Single submitter
- HAVCR2 p.Pro138Arg Uncertain significance Single submitter
- HAVCR2 p.Pro246Leu Uncertain significance Single submitter
- HAVCR2 p.Ser105Gly Uncertain significance Single submitter
- HAVCR2 p.Ser177Thr Uncertain significance Single submitter
- HAVCR2 p.Ser248Leu Uncertain significance Single submitter
- HAVCR2 p.Thr101Ser Uncertain significance Single submitter
- HAVCR2 p.Thr135Ser Uncertain significance Single submitter
- HAVCR2 p.Thr154Ser Uncertain significance Single submitter
- HAVCR2 p.Thr164Arg Uncertain significance Single submitter
- HAVCR2 p.Val49Met Uncertain significance Single submitter
Predictors split 7
The independent predictors disagree with each other — read with care.
- HAVCR2 p.Arg193Trp Uncertain significance Multiple submitters
- HAVCR2 p.Ala189Gly Uncertain significance Single submitter
- HAVCR2 p.Arg184Trp Uncertain significance Single submitter
- HAVCR2 p.Leu188Phe Uncertain significance Single submitter
- HAVCR2 p.Leu36Met Uncertain significance Single submitter
- HAVCR2 p.Phe39Leu Uncertain significance Single submitter
-
HAVCR2 p.Tyr82Cys
Conflicting
Single submitter
Subcutaneous panniculitis T-cell lymphoma (SPTCL)
All HAVCR2 variants
Conflicting classifications of pathogenicity 5
- p.Arg259His Single submitter ⚠
- p.Ile117Leu Single submitter ⚠
- p.Ile97Met Single submitter HAVCR2-related disorder
- p.Thr101Ile Single submitter subcutaneous panniculitis-like T-cell lymphoma ⚠
- p.Tyr82Cys Single submitter Subcutaneous panniculitis T-cell lymphoma (SPTCL) ⚠
Benign 3
- p.Arg140Leu Multiple submitters subcutaneous panniculitis-like T-cell lymphoma
- c.395-105T>C Single submitter
- c.478+116G>A Single submitter
Benign/Likely benign 4
- c.479-30CT[10] Multiple submitters
- c.479-30CT[9] Multiple submitters
- c.714-10A>G Multiple submitters
- p.Pro277Leu Multiple submitters
Likely benign 32
- c.394+13T>G Multiple submitters
- c.479-30CT[12] Multiple submitters
- p.Asn270= Multiple submitters
- p.Asn85= Multiple submitters
- p.Gly156Glu Multiple submitters
- p.Ile107Phe Multiple submitters
- p.Phe298= Multiple submitters
- p.Pro50= Multiple submitters
- c.479-15T>G Single submitter
- c.479-30CT[13] Single submitter
- c.479-30CT[14] Single submitter
- c.58+20T>C Single submitter
- c.59-20C>G Single submitter
- c.677-16G>C Single submitter
- c.713+12G>T Single submitter
- c.714-20G>A Single submitter
- p.Ala28Val Single submitter
- p.Ala43= Single submitter
- p.Arg187Gly Single submitter
- p.Arg297His Single submitter
- p.Arg89His Single submitter
- p.Asn236= Single submitter
- p.Asp92Asn Single submitter
- p.Glu279= Single submitter
- p.Gly196= Single submitter
- p.Ile171Thr Single submitter
- p.Ile205= Single submitter
- p.Leu179= Single submitter
- p.Leu245Ile Single submitter
- p.Pro247= Single submitter
- p.Val128= Single submitter
- p.Gly208Ala No assertion criteria HAVCR2-related disorder
Uncertain significance 48
- p.Arg193Trp Multiple submitters ⚠
- p.Asp170Val Multiple submitters ⚠
- p.Gln175Arg Multiple submitters ⚠
- c.395-2A>T Single submitter subcutaneous panniculitis-like T-cell lymphoma
- c.523-1G>A Single submitter subcutaneous panniculitis-like T-cell lymphoma
- p.Ala147Gly Single submitter ⚠
- p.Ala189Gly Single submitter ⚠
- p.Ala43Pro Single submitter ⚠
- p.Arg111Gln Single submitter subcutaneous panniculitis-like T-cell lymphoma
- p.Arg140Trp Single submitter ⚠
- p.Arg150Gly Single submitter ⚠
- p.Arg184Trp Single submitter ⚠
- p.Arg259Cys Single submitter ⚠
- p.Asn172Lys Single submitter ⚠
- p.Asn172Ser Single submitter ⚠
- p.Asn190Asp Single submitter ⚠
- p.Asn278Ile Single submitter ⚠
- p.Asn278Ser Single submitter ⚠
- p.Asn85Ser Single submitter ⚠
- p.Asp143fs Single submitter
- p.Asp194Gly Single submitter ⚠
- p.Asp71Asn Single submitter ⚠
- p.Asp74Glu Single submitter ⚠
- p.Cys282Gly Single submitter ⚠
- p.Gln163Ter Single submitter
- p.Glu182Lys Single submitter ⚠
- p.Gly64Ser Single submitter ⚠
- p.His157Arg Single submitter ⚠
- p.Ile129Val Single submitter ⚠
- p.Ile205Thr Single submitter ⚠
- p.Ile267Val Single submitter ⚠
- p.Ile97Thr Single submitter ⚠
- p.Leu188Phe Single submitter ⚠
- p.Leu36Met Single submitter ⚠
- p.Lys55Glu Single submitter ⚠
- p.Phe39Leu Single submitter ⚠
- p.Pro138Arg Single submitter ⚠
- p.Pro246Leu Single submitter ⚠
- p.Pro42fs Single submitter
- p.Ser105Gly Single submitter ⚠
- p.Ser177Thr Single submitter ⚠
- p.Ser248Leu Single submitter ⚠
- p.Thr101Ser Single submitter ⚠
- p.Thr135Ser Single submitter ⚠
- p.Thr154Ser Single submitter ⚠
- p.Thr164Arg Single submitter ⚠
- p.Tyr265Ser Single submitter
- p.Val49Met Single submitter ⚠