CALM3 — 194 ClinVar variants
All ClinVar germline CALM3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 33 flagged for review →
6 Pathogenic · 2 Likely pathogenic · 2 Conflicting · 11 Benign · 7 Benign/Likely benign · 115 Likely benign · 51 Uncertain significance
Full CALM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 33
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.
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CALM3 p.Asp132Glu
Conflicting
Single submitter
long QT syndrome 1
Predictors lean, ClinVar uncertain 23
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
CALM3 p.Arg107Cys
Uncertain significance
Multiple submitters
long QT syndrome 1
-
CALM3 p.Asp132Asn
Uncertain significance
Multiple submitters
Cardiovascular phenotype
-
CALM3 p.Gly135Asp
Uncertain significance
Multiple submitters
Cardiovascular phenotype
-
CALM3 p.Gly26Asp
Uncertain significance
Multiple submitters
Cardiovascular phenotype
-
CALM3 p.Thr111Met
Uncertain significance
Multiple submitters
long QT syndrome 1
- CALM3 p.Ala103Thr Uncertain significance Single submitter
-
CALM3 p.Ala103Val
Uncertain significance
Single submitter
long QT syndrome 1
-
CALM3 p.Ala16Gly
Uncertain significance
Single submitter
long QT syndrome 1
- CALM3 p.Arg107His Uncertain significance Single submitter
-
CALM3 p.Asn112Lys
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Asp119Asn
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Asp130His
Uncertain significance
Single submitter
long QT syndrome 1
-
CALM3 p.Asp132Val
Uncertain significance
Single submitter
long QT syndrome 1
-
CALM3 p.Gln42Glu
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Glu124Lys
Uncertain significance
Single submitter
long QT syndrome 1
- CALM3 p.Glu83Lys Uncertain significance Single submitter
-
CALM3 p.Gly62Arg
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Ile126Thr
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Met110Val
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Met146Ile
Uncertain significance
Single submitter
long QT syndrome 1
- CALM3 p.Met72Thr Uncertain significance Single submitter
-
CALM3 p.Met77Val
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Pro44Leu
Uncertain significance
Single submitter
long QT syndrome 1
Predictors split 9
The independent predictors disagree with each other — read with care.
-
CALM3 p.Ala148Thr
Uncertain significance
Multiple submitters
Cardiovascular phenotype
-
CALM3 p.Val109Ile
Uncertain significance
Multiple submitters
long QT syndrome 1
-
CALM3 p.Ala104Thr
Uncertain significance
Single submitter
long QT syndrome 1
-
CALM3 p.Arg91His
Uncertain significance
Single submitter
Cardiovascular phenotype
-
CALM3 p.Asp123Asn
Uncertain significance
Single submitter
long QT syndrome 1
-
CALM3 p.Glu8Asp
Uncertain significance
Single submitter
long QT syndrome 1
-
CALM3 p.Ile28Val
Uncertain significance
Single submitter
long QT syndrome 1
-
CALM3 p.Lys116Arg
Uncertain significance
Single submitter
long QT syndrome 1
- CALM3 p.Tyr100Cys Uncertain significance Single submitter
All CALM3 variants
Pathogenic 6
- p.Asp96His Multiple submitters long QT syndrome 16
- p.Glu141Lys Multiple submitters long QT syndrome 1
- p.Asp130Glu Single submitter long QT syndrome 1
- p.Asp94Ala Single submitter long QT syndrome 1
- p.Phe142Leu Single submitter long QT syndrome 1
- p.Asp130Gly No assertion criteria long QT syndrome 16
Likely pathogenic 2
- p.Asp132Gly Single submitter
- p.Glu141Gly Single submitter long QT syndrome 1
Conflicting classifications of pathogenicity 2
- c.421+4A>G Single submitter long QT syndrome 16
- p.Asp132Glu Single submitter long QT syndrome 1 ⚠
Benign 11
- c.178+66T>C Multiple submitters long QT syndrome 16
- c.34+37G>C Multiple submitters
- c.4-73T>C Multiple submitters long QT syndrome 16
- c.422-24CT[4] Multiple submitters
- c.-14C>A Multiple submitters
- c.*238T>C Multiple submitters
- p.Asp130= Multiple submitters Cardiovascular phenotype
- c.178+19G>A Single submitter long QT syndrome 1
- c.3+18dup Single submitter long QT syndrome 1
- c.34+150G>A Single submitter
- c.35-14C>G Single submitter long QT syndrome 1
Benign/Likely benign 7
- c.178+18C>T Multiple submitters long QT syndrome 1
- c.179-14del Multiple submitters long QT syndrome 1
- c.*9del Multiple submitters
- p.Ala89= Multiple submitters Cardiovascular phenotype
- p.Glu83= Multiple submitters Cardiovascular phenotype
- p.Pro67= Multiple submitters long QT syndrome 1
- p.Ser102= Multiple submitters Cardiovascular phenotype
Likely benign 115
- c.178+17G>A Multiple submitters long QT syndrome 1
- c.3+85A>C Multiple submitters
- c.35-13C>G Multiple submitters long QT syndrome 1
- p.Ala103= Multiple submitters Cardiovascular phenotype
- p.Ala148= Multiple submitters long QT syndrome 1
- p.Arg91= Multiple submitters long QT syndrome 1
- p.Asn61= Multiple submitters long QT syndrome 1
- p.Asp134= Multiple submitters Cardiovascular phenotype
- p.Asp79= Multiple submitters long QT syndrome 1
- p.Gln4= Multiple submitters Cardiovascular phenotype
- p.Gln9= Multiple submitters Cardiovascular phenotype
- p.Glu128= Multiple submitters Cardiovascular phenotype
- p.Glu55= Multiple submitters Cardiovascular phenotype
- p.Glu8= Multiple submitters long QT syndrome 1
- p.His108= Multiple submitters Cardiovascular phenotype
- p.Leu106= Multiple submitters Cardiovascular phenotype
- p.Leu33= Multiple submitters long QT syndrome 1
- p.Thr118= Multiple submitters Cardiovascular phenotype
- p.Val122= Multiple submitters long QT syndrome 1
- c.178+12A>G Single submitter long QT syndrome 1
- c.178+16C>T Single submitter long QT syndrome 1
- c.178+48G>A Single submitter
- c.179-11C>T Single submitter long QT syndrome 1
- c.179-13C>T Single submitter long QT syndrome 1
- c.179-18C>T Single submitter long QT syndrome 1
- c.285+16C>T Single submitter long QT syndrome 1
- c.285+17A>G Single submitter long QT syndrome 1
- c.285+9C>A Single submitter long QT syndrome 1
- c.286-10C>G Single submitter long QT syndrome 1
- c.286-19C>G Single submitter long QT syndrome 1
- c.286-4C>G Single submitter long QT syndrome 1
- c.286-7C>A Single submitter long QT syndrome 1
- c.286-8dup Single submitter long QT syndrome 1
- c.3+11C>T Single submitter long QT syndrome 1
- c.3+13G>A Single submitter long QT syndrome 1
- c.3+14G>C Single submitter long QT syndrome 1
- c.3+16G>A Single submitter long QT syndrome 1
- c.3+17G>A Single submitter long QT syndrome 1
- c.3+18G>A Single submitter long QT syndrome 1
- c.3+19T>G Single submitter long QT syndrome 1
- c.3+20C>T Single submitter long QT syndrome 1
- c.34+11T>C Single submitter long QT syndrome 1
- c.34+13T>C Single submitter long QT syndrome 1
- c.34+16C>T Single submitter long QT syndrome 1
- c.34+7C>G Single submitter long QT syndrome 1
- c.35-10C>T Single submitter long QT syndrome 1
- c.35-13C>A Single submitter long QT syndrome 1
- c.35-146G>A Single submitter
- c.35-14C>A Single submitter long QT syndrome 1
- c.35-14C>T Single submitter long QT syndrome 1
- c.35-16C>T Single submitter long QT syndrome 1
- c.35-179G>A Single submitter
- c.35-18T>C Single submitter long QT syndrome 1
- c.35-18T>G Single submitter long QT syndrome 1
- c.35-19C>T Single submitter long QT syndrome 1
- c.35-9T>C Single submitter long QT syndrome 1
- c.4-12A>T Single submitter long QT syndrome 1
- c.4-162G>A Single submitter
- c.4-17C>G Single submitter long QT syndrome 1
- c.4-17C>T Single submitter long QT syndrome 1
- c.4-304G>A Single submitter
- c.4-5T>C Single submitter long QT syndrome 1
- c.4-6T>C Single submitter long QT syndrome 1
- c.421+10G>T Single submitter long QT syndrome 1
- c.421+14A>G Single submitter long QT syndrome 1
- c.421+15G>C Single submitter long QT syndrome 1
- c.421+16G>A Single submitter long QT syndrome 1
- c.421+16G>C Single submitter long QT syndrome 1
- c.421+16G>T Single submitter long QT syndrome 1
- c.421+18T>C Single submitter long QT syndrome 1
- c.422-18C>T Single submitter long QT syndrome 1
- c.422-20C>G Single submitter long QT syndrome 1
- c.422-5C>T Single submitter long QT syndrome 1
- c.422-7_422-3del Single submitter long QT syndrome 1
- c.422-7T>C Single submitter long QT syndrome 1
- c.422-8C>T Single submitter long QT syndrome 1
- c.422-9A>G Single submitter long QT syndrome 1
- c.-106+82G>A Single submitter
- c.-29C>T Single submitter
- c.*19G>A Single submitter
- c.*21G>C Single submitter
- p.Ala129= Single submitter long QT syndrome 1
- p.Ala58= Single submitter long QT syndrome 1
- p.Ala74= Single submitter long QT syndrome 1
- p.Asn112= Single submitter
- p.Asp119= Single submitter long QT syndrome 1
- p.Asp25= Single submitter long QT syndrome 1
- p.Asp3= Single submitter long QT syndrome 1
- p.Asp57= Single submitter
- p.Asp94= Single submitter long QT syndrome 1
- p.Glu120= Single submitter Cardiovascular phenotype
- p.Glu121= Single submitter long QT syndrome 1
- p.Glu46= Single submitter long QT syndrome 1
- p.Glu48= Single submitter long QT syndrome 1
- p.Glu84= Single submitter long QT syndrome 1
- p.Gly114= Single submitter long QT syndrome 1
- p.Gly24= Single submitter long QT syndrome 1
- p.Ile131= Single submitter long QT syndrome 1
- p.Ile53= Single submitter long QT syndrome 1
- p.Ile64= Single submitter long QT syndrome 1
- p.Leu113= Single submitter Cardiovascular phenotype
- p.Leu19= Single submitter long QT syndrome 1
- p.Leu49= Single submitter long QT syndrome 1
- p.Lys149= Single submitter long QT syndrome 1
- p.Lys22= Single submitter long QT syndrome 1
- p.Phe142= Single submitter long QT syndrome 1
- p.Phe17= Single submitter long QT syndrome 1
- p.Pro44= Single submitter long QT syndrome 1
- p.Ser82= Single submitter Cardiovascular phenotype
- p.Thr111= Single submitter long QT syndrome 1
- p.Thr27= Single submitter long QT syndrome 1
- p.Thr71= Single submitter long QT syndrome 1
- p.Val137= Single submitter Cardiovascular phenotype
- p.Val143= Single submitter long QT syndrome 1
- p.Val36= Single submitter long QT syndrome 1
Uncertain significance 51
- c.179-3del Multiple submitters long QT syndrome 16
- c.34+3G>A Multiple submitters Cardiovascular phenotype
- c.421+5G>A Multiple submitters Cardiovascular phenotype
- p.Ala148Thr Multiple submitters Cardiovascular phenotype ⚠
- p.Arg107Cys Multiple submitters long QT syndrome 1 ⚠
- p.Asp132Asn Multiple submitters Cardiovascular phenotype ⚠
- p.Gly135Asp Multiple submitters Cardiovascular phenotype ⚠
- p.Gly26Asp Multiple submitters Cardiovascular phenotype ⚠
- p.Thr111Met Multiple submitters long QT syndrome 1 ⚠
- p.Val109Ile Multiple submitters long QT syndrome 1 ⚠
- c.178+3G>A Single submitter Cardiovascular phenotype
- c.286-16T>C Single submitter long QT syndrome 1
- c.3+774G>C Single submitter
- c.3+774G>T Single submitter
- c.34+4A>G Single submitter long QT syndrome 1
- c.4-3C>T Single submitter long QT syndrome 1
- c.421+6T>G Single submitter long QT syndrome 1
- c.422-3_422-2del Single submitter long QT syndrome 1
- c.-3G>A Single submitter Cardiovascular phenotype
- c.-3G>T Single submitter
- c.-6C>A Single submitter
- c.*1A>G Single submitter Cardiovascular phenotype
- p.Ala103Thr Single submitter ⚠
- p.Ala103Val Single submitter long QT syndrome 1 ⚠
- p.Ala104Thr Single submitter long QT syndrome 1 ⚠
- p.Ala16Gly Single submitter long QT syndrome 1 ⚠
- p.Arg107His Single submitter ⚠
- p.Arg87Ter Single submitter long QT syndrome 1
- p.Arg91His Single submitter Cardiovascular phenotype ⚠
- p.Asn112Lys Single submitter Cardiovascular phenotype ⚠
- p.Asn43fs Single submitter long QT syndrome 1
- p.Asp119Asn Single submitter Cardiovascular phenotype ⚠
- p.Asp123Asn Single submitter long QT syndrome 1 ⚠
- p.Asp130His Single submitter long QT syndrome 1 ⚠
- p.Asp132Val Single submitter long QT syndrome 1 ⚠
- p.Asp59= Single submitter long QT syndrome 1
- p.Gln42Glu Single submitter Cardiovascular phenotype ⚠
- p.Glu124Lys Single submitter long QT syndrome 1 ⚠
- p.Glu83Lys Single submitter ⚠
- p.Glu8Asp Single submitter long QT syndrome 1 ⚠
- p.Gly62Arg Single submitter Cardiovascular phenotype ⚠
- p.Ile126Thr Single submitter Cardiovascular phenotype ⚠
- p.Ile28Val Single submitter long QT syndrome 1 ⚠
- p.Lys116Arg Single submitter long QT syndrome 1 ⚠
- p.Lys14= Single submitter Cardiovascular phenotype
- p.Met110Val Single submitter Cardiovascular phenotype ⚠
- p.Met146Ile Single submitter long QT syndrome 1 ⚠
- p.Met72Thr Single submitter ⚠
- p.Met77Val Single submitter Cardiovascular phenotype ⚠
- p.Pro44Leu Single submitter long QT syndrome 1 ⚠
- p.Tyr100Cys Single submitter ⚠