CALM3 (Calmodulin-3) variants and mutations
CALM3 (also known as Calmodulin-3) is a human protein-coding gene encoding a calmodulin-3 protein. It produces the same highly conserved calmodulin protein as CALM1 and CALM2, allowing calcium-dependent regulation of many cardiac and neuronal proteins. Pathogenic missense variants can cause severe inherited arrhythmia syndromes collectively termed calmodulinopathies. This analysis covers 231 CALM3 variants and mutations. Of these, 68% have computational variant effect predictions. Disease context includes long QT syndrome 16, long QT syndrome 1, and bacterial infectious disease. Example CALM3 variants include M1?, A2S, and A2A.
Variant analysis overview
- Gene: CALM3
- Protein: Calmodulin-3
- UniProt accession: P0DP25
- Organism: Homo sapiens
- Variants analyzed: 231
- Variant scope: all variants
- Completed: 2026-08-20
Variant and mutation evidence
- Variant composition: 212 unspecified-consequence records; 3 missense variants; 1 splice-region variants; 6 synonymous variants; 9 substitution
- Prediction scores: 157 variants have prediction scores (68% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: long QT syndrome 16, long QT syndrome 1, bacterial infectious disease, Prolonged QT interval, familial long QT syndrome, neurodegenerative disease, Romano-Ward syndrome, catecholaminergic polymorphic ventricular tachycardia, Abnormality of the cardiovascular system, atrial fibrillation, prostatitis, eye injury.
Protein structure and variant hotspots
- Protein features: 4 domains; 20 binding sites; 11 post-translational modification sites.
- Structural context: 207 variants have structural context.
- PTM context: 12 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable CALM3 variants
Examples include M1?, A2S, A2A, D3E, D3H, D3N, D3D, Q4L. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- A2S (p.Ala2Ser), gnomAD 19-46605827-G-T, REVEL 0.23, MetaLR 0.09
- A2A (p.Ala2Ala), rs1971731490, gnomAD 19-46605829-T-C, CADD 17.90
- D3E (p.Asp3Glu), TOPMed rs1463101364, gnomAD rs1463101364
- D3H (p.Asp3His), cosmic curated COSV10501, NCI-TCGA TCGA novel, MetaLR 0.09, MetaSVM -0.94, Variant assessed as somatic; moderate impact.
- D3N (p.Asp3Asn), ExAC rs778455345, gnomAD rs778455345, REVEL 0.21, MetaLR 0.09
- D3D (p.Asp3Asp), rs1463101364, gnomAD 19-46605832-C-T, CADD 12.70
- Q4L (p.Gln4Leu), gnomAD 19-46605834-A-T, REVEL 0.27, MetaLR 0.08
- Q4Q (p.Gln4Gln), rs746427314, gnomAD 19-46605835-G-A, CADD 11.90
- L5M (p.Leu5Met), Ensembl rs1886977818, MetaLR 0.25, MetaSVM -0.51
- L5L (p.Leu5Leu), gnomAD 19-46605838-G-T, CADD 13.80
- T6I (p.Thr6Ile), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10081, Variant assessed as somatic; moderate impact.
- T6S (p.Thr6Ser), gnomAD rs1439126449, MetaLR 0.09, MetaSVM -0.98, Uncertain significance
- T6T (p.Thr6Thr), gnomAD 19-46605841-T-G, CADD 2.23
- E8* (p.Glu8Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- E8D (p.Glu8Asp), rs1001080500, ClinGen CA406470843, ClinVar RCV002003340, TOPMed rs1001080500, REVEL 0.08, MetaLR 0.11, Uncertain significance, Long QT syndrome 1
- E8E (p.Glu8Glu), rs1001080500, gnomAD 19-46605847-G-A, CADD 11.70
- Q9H (p.Gln9His), NCI-TCGA Cosmic COSV5539, cosmic curated COSV55398, NCI-TCGA Cosmic COSV5219, cosmic curated COSV52194, MetaLR 0.64, MetaSVM 0.27, Variant assessed as somatic; moderate impact.
- Q9Q (p.Gln9Gln), rs1971731867, gnomAD 19-46605850-G-A, CADD 11.80
- I10M (p.Ile10Met), cosmic curated COSV52194
- I10T (p.Ile10Thr), ESP rs373571763, REVEL 0.82, MetaLR 0.66
- I10V (p.Ile10Val), ExAC rs765365900, gnomAD rs765365900, MetaLR 0.48, MetaSVM 0.01, Uncertain significance
- I10F (p.Ile10Phe), gnomAD 19-46605851-A-T, REVEL 0.76, MetaLR 0.68
- A11S (p.Ala11Ser), TOPMed rs1886978741, MetaLR 0.56, MetaSVM 0.22
- A11T (p.Ala11Thr), NCI-TCGA Cosmic COSV9935, cosmic curated COSV99355, REVEL 0.55, MetaLR 0.56, Variant assessed as somatic; moderate impact.
- E12* (p.Glu12Ter), cosmic curated COSV99355
- E12G (p.Glu12Gly), NCI-TCGA Cosmic COSV9935, cosmic curated COSV99355, Variant assessed as somatic; moderate impact.
- F13L (p.Phe13Leu), NCI-TCGA Cosmic COSV5540, cosmic curated COSV55400, REVEL 0.65, MetaLR 0.33, Variant assessed as somatic; moderate impact.
- F13V (p.Phe13Val), NCI-TCGA TCGA novel, MetaLR 0.57, MetaSVM 0.23, Variant assessed as somatic; moderate impact.
- K14E (p.Lys14Glu), gnomAD rs1354288400
- K14R (p.Lys14Arg), gnomAD rs1307543946, MetaLR 0.64, MetaSVM 0.37
- E15* (p.Glu15Ter), NCI-TCGA Cosmic COSV5539, cosmic curated COSV55399, Variant assessed as somatic; high impact.
- E15D (p.Glu15Asp), TOPMed rs1366326090, gnomAD rs1366326090, REVEL 0.52, MetaLR 0.70
- E15G (p.Glu15Gly), cosmic curated COSV10462, MetaLR 0.86, MetaSVM 0.89
- A16G (p.Ala16Gly), rs1599758635, ClinGen CA406471673, ClinVar RCV004577345, Ensembl rs1599758635, AlphaMissense 0.90, MetaLR 0.73, Uncertain significance, Long QT syndrome 1
- A16T (p.Ala16Thr), gnomAD rs1462073630, MetaLR 0.66, MetaSVM 0.41
- S18L (p.Ser18Leu), ExAC rs778389067, gnomAD rs778389067, MetaLR 0.37, MetaSVM -0.28
- L19V (p.Leu19Val), NCI-TCGA Cosmic COSV5539, MetaLR 0.56, MetaSVM 0.12, Variant assessed as somatic; moderate impact.
- D21G (p.Asp21Gly), rs2503454528, ClinGen CA390689267, ClinVar RCV002368771, Uncertain significance
- D21N (p.Asp21Asn), cosmic curated COSV10955, Ensembl rs976949001, MetaLR 0.95, MetaSVM 1.09
- D23E (p.Asp23Glu), cosmic curated COSV52194, REVEL 0.65, MetaLR 0.54
- D23G (p.Asp23Gly), rs11551457, ClinGen CA46691730, ClinVar RCV004434591, NCI-TCGA Cosmic COSV9970, Uncertain significance
- D23Y (p.Asp23Tyr), rs1064795808, ClinGen CA16619891, ClinVar RCV000483941, Ensembl rs1064795808, MetaLR 0.65, MetaSVM 0.45, Uncertain significance
- G24A (p.Gly24Ala), ExAC rs112786165, TOPMed rs112786165, gnomAD rs112786165
- G24D (p.Gly24Asp), ExAC rs112786165, TOPMed rs112786165, gnomAD rs112786165
- G24R (p.Gly24Arg), TOPMed rs1971785461
- G24S (p.Gly24Ser), rs2503454539, ClinGen CA390689286, ClinVar RCV002923465, Uncertain significance
- G24V (p.Gly24Val), ExAC rs112786165, TOPMed rs112786165, gnomAD rs112786165
- G26C (p.Gly26Cys), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10081, Variant assessed as somatic; moderate impact.
- G26D (p.Gly26Asp), rs1971785540, ClinGen CA406471820, ClinVar RCV002409903, ClinVar RCV005620448, REVEL 0.85, MetaLR 0.89, Uncertain significance, not provided; Cardiovascular phenotype
- G26E (p.Gly26Glu), NCI-TCGA Cosmic COSV5540, cosmic curated COSV55400, Variant assessed as somatic; moderate impact.
- G26V (p.Gly26Val), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10081, MetaLR 0.95, MetaSVM 1.09, Variant assessed as somatic; moderate impact.
- T27S (p.Thr27Ser), rs1131691669, ClinGen CA346720087, ClinVar RCV000493725, ClinVar RCV001856970, AlphaMissense 0.30, MetaLR 0.49, Uncertain significance
- I28V (p.Ile28Val), rs763100441, NCI-TCGA Cosmic COSV5219, cosmic curated COSV52195, ExAC rs763100441, REVEL 0.59, MetaLR 0.60, Uncertain significance, Long QT syndrome 1
- T30P (p.Thr30Pro), rs1057521851, ClinGen CA16606882, ClinVar RCV000431318, Ensembl rs1057521851, MetaLR 0.63, MetaSVM 0.31, Likely pathogenic
- T30S (p.Thr30Ser), cosmic curated COSV52194, MetaLR 0.46, MetaSVM -0.01
- K31E (p.Lys31Glu), NCI-TCGA Cosmic COSV6366, cosmic curated COSV63663, MetaLR 0.46, MetaSVM -0.00, Variant assessed as somatic; moderate impact.
- E32Q (p.Glu32Gln), Ensembl rs2122245414, MetaLR 0.77, MetaSVM 0.66
- L33F (p.Leu33Phe), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- L33V (p.Leu33Val), TOPMed rs1887014864
- T35I (p.Thr35Ile), rs757523692, ClinGen CA1648594, ClinVar RCV002272427, ClinVar RCV002402782, AlphaMissense 0.89, MetaLR 0.75, Uncertain significance
- T35N (p.Thr35Asn), rs757523692, ClinGen CA346720022, ClinVar RCV003224656, AlphaMissense 0.89, MetaLR 0.75, Uncertain significance
- V36A (p.Val36Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V36L (p.Val36Leu), rs1887015236, ClinGen CA390689365, ClinVar RCV001048231, Ensembl rs1887015236, MetaLR 0.65, MetaSVM 0.30, Uncertain significance
- M37I (p.Met37Ile), Ensembl rs11551432
- R38G (p.Arg38Gly), rs766892006, []
- S39P (p.Ser39Pro), Ensembl rs11551458
- S39Y (p.Ser39Tyr), NCI-TCGA Cosmic COSV5539, cosmic curated COSV55399, Variant assessed as somatic; moderate impact.
- L40P (p.Leu40Pro), 1000Genomes rs199950662, MetaLR 0.37, MetaSVM -0.09
- G41S (p.Gly41Ser), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q42* (p.Gln42Ter), ExAC rs775591771, gnomAD rs775591771, CADD 37.00
- Q42E (p.Gln42Glu), rs775591771, ClinGen CA406472016, ClinVar RCV004434592, Uncertain significance, Cardiovascular phenotype
- Q42L (p.Gln42Leu), 1000Genomes rs199897752
- Q42R (p.Gln42Arg), Ensembl rs11551442, MetaLR 0.29, MetaSVM -0.47
- P44L (p.Pro44Leu), rs1599758674, ClinGen CA406472055, ClinVar RCV002234358, Ensembl rs1599758674, AlphaMissense 0.98, MetaLR 0.49, Uncertain significance, Long QT syndrome 1
- P44R (p.Pro44Arg), rs2465709286, ClinGen CA346719932, ClinVar RCV004511096, Uncertain significance
- P44S (p.Pro44Ser), rs2465709290, ClinGen CA346719935, ClinVar RCV002385401, Uncertain significance
- T45P (p.Thr45Pro), Ensembl rs1687190786, MetaLR 0.57, MetaSVM 0.21
- E46K (p.Glu46Lys), rs2465709282, ClinGen CA346719917, ClinVar RCV003391395, Uncertain significance
- E48* (p.Glu48Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- E48K (p.Glu48Lys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- E48V (p.Glu48Val), cosmic curated COSV99355, MetaLR 0.71, MetaSVM 0.55
- Q50H (p.Gln50His), NCI-TCGA Cosmic COSV9935, cosmic curated COSV99355, Variant assessed as somatic; moderate impact.
- Q50P (p.Gln50Pro), ExAC rs11551450, gnomAD rs11551450
- Q50R (p.Gln50Arg), ExAC rs11551450, gnomAD rs11551450, MetaLR 0.16, MetaSVM -0.64
- D51GfsX5, rs749917251, []
- M52V (p.Met52Val), NCI-TCGA Cosmic COSV9935, cosmic curated COSV99355, MetaLR 0.37, MetaSVM -0.25, Variant assessed as somatic; moderate impact.
- I53V (p.Ile53Val), rs1553431807, ClinGen CA346719813, ClinVar RCV000555733, Ensembl rs1553431807, AlphaMissense 0.46, MetaLR 0.49, Uncertain significance
- N54D (p.Asn54Asp), cosmic curated COSV10439, REVEL 0.56, MetaLR 0.18
- N54I (p.Asn54Ile), rs267607276, ClinGen CA343809, ClinVar RCV000032976, ClinVar RCV000157133, AlphaMissense 0.11, MetaLR 0.32, Pathogenic
- N54S (p.Asn54Ser), cosmic curated COSV10968, TOPMed rs267607276, gnomAD rs267607276, MetaLR 0.18, MetaSVM -0.63, Likely pathogenic
- D57N (p.Asp57Asn), NCI-TCGA TCGA novel, MetaLR 0.88, MetaSVM 0.99, Variant assessed as somatic; moderate impact.
- A58P (p.Ala58Pro), rs2103825594, ClinGen CA346719732, ClinVar RCV001765233, ClinVar RCV005094951, AlphaMissense 0.99, MetaLR 0.75, Uncertain significance
- D59H (p.Asp59His), NCI-TCGA Cosmic COSV9970, cosmic curated COSV99700, REVEL 0.76, MetaLR 0.60, Variant assessed as somatic; moderate impact.
- G60R (p.Gly60Arg), NCI-TCGA Cosmic COSV9935, cosmic curated COSV99355, MetaLR 0.57, MetaSVM 0.18, Variant assessed as somatic; moderate impact.
- N61H (p.Asn61His), cosmic curated COSV10501
- N61S (p.Asn61Ser), rs2103825319, ClinGen CA346719643, ClinVar RCV001873853, Ensembl rs2103825319, AlphaMissense 0.22, MetaLR 0.49, Uncertain significance
- G62D (p.Gly62Asp), NCI-TCGA Cosmic COSV5539, cosmic curated COSV55399, MetaLR 0.75, MetaSVM 0.68, Variant assessed as somatic; moderate impact.
- G62R (p.Gly62Arg), cosmic curated COSV52194, ExAC rs762484332, TOPMed rs762484332, gnomAD rs762484332, REVEL 0.87, MetaLR 0.78, Uncertain significance, Cardiovascular phenotype
- D65H (p.Asp65His), NCI-TCGA Cosmic COSV5540, cosmic curated COSV55400, MetaLR 0.68, MetaSVM 0.47, Variant assessed as somatic; moderate impact.
- P67L (p.Pro67Leu), NCI-TCGA Cosmic COSV6366, cosmic curated COSV63663, Ensembl rs1971792952, Variant assessed as somatic; moderate impact.
- P67Q (p.Pro67Gln), cosmic curated COSV10879
- P67S (p.Pro67Ser), gnomAD rs1373581301, MetaLR 0.40, MetaSVM -0.05
- E68* (p.Glu68Ter), NCI-TCGA Cosmic COSV6366, cosmic curated COSV63662, Variant assessed as somatic; high impact.
- E68A (p.Glu68Ala), rs1687186092, ClinGen CA346719535, ClinVar RCV002242197, Ensembl rs1687186092, AlphaMissense 0.99, MetaLR 0.75, Uncertain significance
- E68K (p.Glu68Lys), NCI-TCGA Cosmic COSV6366, cosmic curated COSV63663, MetaLR 0.80, MetaSVM 0.79, Variant assessed as somatic; moderate impact.
- L70F (p.Leu70Phe), rs2503458538, NCI-TCGA Cosmic COSV6366, cosmic curated COSV63662, ClinGen CA390689901, Uncertain significance
- M72L (p.Met72Leu), NCI-TCGA Cosmic COSV9935, cosmic curated COSV99355, Variant assessed as somatic; moderate impact.
- M72T (p.Met72Thr), NCI-TCGA TCGA novel, REVEL 0.75, MetaLR 0.44, Uncertain significance, not provided
- M72V (p.Met72Val), rs2465708894, ClinGen CA346719501, ClinVar RCV004148688, Uncertain significance
- M73I (p.Met73Ile), NCI-TCGA Cosmic COSV9935, cosmic curated COSV99355, NCI-TCGA Cosmic COSV6366, cosmic curated COSV63663, MetaLR 0.46, MetaSVM -0.05, Variant assessed as somatic; moderate impact.
- A74T (p.Ala74Thr), NCI-TCGA TCGA novel, MetaLR 0.15, MetaSVM -0.90, Variant assessed as somatic; moderate impact.
- K76N (p.Lys76Asn), TOPMed rs1156698660, MetaLR 0.67, MetaSVM 0.36
- M77I (p.Met77Ile), gnomAD rs1333482396, REVEL 0.64, MetaLR 0.47
- M77V (p.Met77Val), NCI-TCGA Cosmic COSV5539, cosmic curated COSV55398, MetaLR 0.51, MetaSVM 0.06, Uncertain significance, Cardiovascular phenotype
- D79E (p.Asp79Glu), NCI-TCGA Cosmic COSV5540, cosmic curated COSV55400, MetaLR 0.22, MetaSVM -0.90, Variant assessed as somatic; moderate impact.
- S82R (p.Ser82Arg), ExAC rs753602780, gnomAD rs753602780, MetaLR 0.49, MetaSVM -0.08
- E83K (p.Glu83Lys), rs2513645057, ClinGen CA406472670, ClinVar RCV003443269, NCI-TCGA Cosmic COSV1008, Uncertain significance, not provided
- R87* (p.Arg87Ter), rs1044180500, ClinGen CA406472733, ClinVar RCV002810356, cosmic curated COSV99059, CADD 37.00, Uncertain significance
- R87H (p.Arg87His), rs2503458623, ClinGen CA390690028, ClinVar RCV002437171, ClinVar RCV004812451, Uncertain significance
- R87Q (p.Arg87Gln), rs1307420144, NCI-TCGA Cosmic COSV5219, cosmic curated COSV52194, gnomAD rs1307420144, REVEL 0.61, MetaLR 0.58, Variant assessed as somatic; moderate impact.
- A89T (p.Ala89Thr), NCI-TCGA TCGA novel, MetaLR 0.75, MetaSVM 0.66, Variant assessed as somatic; moderate impact.
- A89V (p.Ala89Val), ExAC rs756526606, gnomAD rs756526606, REVEL 0.81, MetaLR 0.71
- F90L (p.Phe90Leu), rs2465708816, ClinGen CA346719361, ClinVar RCV003501689, Likely pathogenic
- R91* (p.Arg91Ter), NCI-TCGA Cosmic COSV6366, cosmic curated COSV63662, Variant assessed as somatic; high impact.
- R91C (p.Arg91Cys), cosmic curated COSV99700, Ensembl rs1687185440, cosmic curated COSV52194, REVEL 0.58, MetaLR 0.70
- R91H (p.Arg91His), gnomAD rs1971794358, REVEL 0.68, MetaLR 0.67, Uncertain significance, Cardiovascular phenotype
- R91L (p.Arg91Leu), rs2103825224, ClinGen CA346719349, ClinVar RCV003982609, AlphaMissense 0.51, MetaLR 0.78, Uncertain significance
- R91Q (p.Arg91Gln), Ensembl rs11541171
- R91S (p.Arg91Ser), cosmic curated COSV99355, MetaLR 0.47, MetaSVM -0.04
- V92E (p.Val92Glu), gnomAD rs1687185375, MetaLR 0.71, MetaSVM 0.54
- F93L (p.Phe93Leu), NCI-TCGA TCGA novel, MetaLR 0.31, MetaSVM -0.40, Variant assessed as somatic; moderate impact.
- D94A (p.Asp94Ala), rs1060502608, ClinGen CA16616071, ClinVar RCV000475293, ClinVar RCV000786284, AlphaMissense 1.00, MetaLR 0.94, Pathogenic/Likely pathogenic, Long QT syndrome 1; not provided
- D94H (p.Asp94His), rs1887099943, ClinGen CA390690072, ClinVar RCV001216383, Ensembl rs1887099943, AlphaMissense 0.99, MetaLR 0.93, Uncertain significance, Long QT syndrome 1
- D94N (p.Asp94Asn), NCI-TCGA TCGA novel, MetaLR 0.96, MetaSVM 1.09, Uncertain significance, Cardiovascular phenotype
- K95E (p.Lys95Glu), NCI-TCGA Cosmic COSV5540, cosmic curated COSV55400, MetaLR 0.58, MetaSVM 0.24, Variant assessed as somatic; moderate impact.
- D96G (p.Asp96Gly), rs2139771574, ClinGen CA390690101, ClinVar RCV002211276, Ensembl rs2139771574, AlphaMissense 0.83, MetaLR 0.20, Likely pathogenic, not provided
- D96H (p.Asp96His), rs1060502607, ClinGen CA16616292, ClinVar RCV002230393, ClinVar RCV004594063, AlphaMissense 0.99, MetaLR 0.62, Pathogenic, Long QT syndrome 16; Long QT syndrome 1
- D96V (p.Asp96Val), rs730882254, ClinGen CA186019, ClinVar RCV000162065, ClinVar RCV001547926, AlphaMissense 0.99, MetaLR 0.31, Uncertain significance, Long QT syndrome 1
- D96Y (p.Asp96Tyr), rs2503459594, ClinGen CA390690100, ClinVar RCV003025983, Pathogenic
- G97A (p.Gly97Ala), NCI-TCGA Cosmic COSV5539, cosmic curated COSV55399, MetaLR 0.78, MetaSVM 0.73, Variant assessed as somatic; moderate impact.
- N98I (p.Asn98Ile), rs398124647, ClinGen CA186027, ClinVar RCV000143837, ClinVar RCV000162068, AlphaMissense 0.29, MetaLR 0.49, Pathogenic
- N98K (p.Asn98Lys), cosmic curated COSV52195
- N98S (p.Asn98Ser), rs267607277, ClinGen CA343812, ClinVar RCV000032977, ClinVar RCV000157134, AlphaMissense 0.14, MetaLR 0.31, Pathogenic
- G99V (p.Gly99Val), NCI-TCGA TCGA novel, REVEL 0.86, MetaLR 0.86, Variant assessed as somatic; moderate impact.
- Y100* (p.Tyr100Ter), ExAC rs749089456, TOPMed rs749089456, gnomAD rs749089456, CADD 36.00
- Y100C (p.Tyr100Cys), rs2503459622, ClinGen CA390690129, ClinVar RCV002300847, Uncertain significance, not provided
- Y100F (p.Tyr100Phe), Ensembl rs1573214341, MetaLR 0.23, MetaSVM -0.56, Uncertain significance
- Y100X, rs749089456, []
- I101M (p.Ile101Met), NCI-TCGA Cosmic COSV5219, cosmic curated COSV52194, Variant assessed as somatic; moderate impact.
- I101N (p.Ile101Asn), gnomAD rs1480930765, MetaLR 0.77, MetaSVM 0.81
- I101V (p.Ile101Val), rs1595102592, ClinGen CA390690134, ClinVar RCV000798107, Ensembl rs1595102592, REVEL 0.52, MetaLR 0.39, Uncertain significance
- A103T (p.Ala103Thr), rs147880865, ClinGen CA9529818, ClinVar RCV001757345, ESP rs147880865, REVEL 0.73, MetaLR 0.53, Uncertain significance, not provided
- A103V (p.Ala103Val), rs1568666713, ClinGen CA406473026, ClinVar RCV000702453, Ensembl rs1568666713, REVEL 0.83, MetaLR 0.48, Uncertain significance, Long QT syndrome 1
- A104T (p.Ala104Thr), rs767096742, ClinGen CA9529820, ClinVar RCV003087145, ExAC rs767096742, REVEL 0.23, MetaLR 0.10, Uncertain significance, Long QT syndrome 1
- A104V (p.Ala104Val), rs11551437, ClinGen CA46690850, ClinVar RCV002320471, Ensembl rs11551437, AlphaMissense 0.81, MetaLR 0.26, Uncertain significance
- E105K (p.Glu105Lys), rs1057523130, ClinGen CA16606883, ClinVar RCV000442999, Ensembl rs1057523130, AlphaMissense 0.98, MetaLR 0.65, Pathogenic, Long QT syndrome 1; Long QT syndrome 16
- E105Q (p.Glu105Gln), rs2465707237, ClinGen CA346719247, ClinVar RCV003224832, cosmic curated COSV52194, Likely pathogenic
- R107C (p.Arg107Cys), rs1599759441, ClinGen CA406473067, NCI-TCGA Cosmic COSV5219, cosmic curated COSV52194, REVEL 0.89, MetaLR 0.78, Uncertain significance, not provided; Long QT syndrome 1
- R107H (p.Arg107His), rs1398867574, ClinGen CA406473073, NCI-TCGA Cosmic COSV5219, cosmic curated COSV52194, REVEL 0.86, MetaLR 0.76, Uncertain significance, not provided
- H108D (p.His108Asp), rs2139771617, ClinGen CA390690178, ClinVar RCV002224275, Ensembl rs2139771617, AlphaMissense 0.93, MetaLR 0.59, Uncertain significance
- V109I (p.Val109Ile), rs1199451414, NCI-TCGA Cosmic COSV1008, cosmic curated COSV10081, gnomAD rs1199451414, REVEL 0.47, MetaLR 0.61, Uncertain significance, Long QT syndrome 1; Cardiovascular phenotype
- V109L (p.Val109Leu), NCI-TCGA TCGA novel, REVEL 0.71, MetaLR 0.57, Variant assessed as somatic; moderate impact.
- M110L (p.Met110Leu), rs2139771638, ClinGen CA390690191, ClinVar RCV001921674, Ensembl rs2139771638, AlphaMissense 0.49, MetaLR 0.42, Uncertain significance
- T111M (p.Thr111Met), rs764512871, ClinGen CA9529823, ClinVar RCV003608438, ClinVar RCV006272523, REVEL 0.39, MetaLR 0.37, Uncertain significance, Long QT syndrome 1; not provided
- N112D (p.Asn112Asp), NCI-TCGA Cosmic COSV9970, cosmic curated COSV99700, MetaLR 0.28, MetaSVM -0.46, Variant assessed as somatic; moderate impact.
- G114R (p.Gly114Arg), rs2103823712, ClinGen CA346719185, ClinVar RCV001787705, Ensembl rs2103823712, AlphaMissense 1.00, MetaLR 0.35, Pathogenic
- G114W (p.Gly114Trp), cosmic curated COSV99355
- E115D (p.Glu115Asp), NCI-TCGA Cosmic COSV9970, cosmic curated COSV99700, Variant assessed as somatic; moderate impact.
- E115K (p.Glu115Lys), NCI-TCGA Cosmic COSV5539, cosmic curated COSV55399, MetaLR 0.45, MetaSVM -0.05, Variant assessed as somatic; moderate impact.
- L117S (p.Leu117Ser), rs2465707170, ClinGen CA346719160, ClinVar RCV003210169, Uncertain significance
- D119N (p.Asp119Asn), rs2122249750, ClinGen CA406473271, ClinVar RCV002454925, Ensembl rs2122249750, REVEL 0.38, MetaLR 0.47, Uncertain significance, Cardiovascular phenotype
- E120D (p.Glu120Asp), Ensembl rs1687165583
- E120K (p.Glu120Lys), rs2503459716, ClinGen CA390690262, ClinVar RCV002299569, ClinVar RCV005626634, Uncertain significance
- V122G (p.Val122Gly), Ensembl rs1599759512, MetaLR 0.34, MetaSVM -0.26
- D123G (p.Asp123Gly), cosmic curated COSV10962, MetaLR 0.29, MetaSVM -0.43
- D123N (p.Asp123Asn), rs2122249867, ClinGen CA406473365, ClinVar RCV001896263, Ensembl rs2122249867, REVEL 0.25, MetaLR 0.23, Uncertain significance, Long QT syndrome 1
- E124K (p.Glu124Lys), rs2513645822, ClinGen CA406473384, ClinVar RCV002785277, REVEL 0.36, MetaLR 0.22, Uncertain significance, Long QT syndrome 1
- E124Q (p.Glu124Gln), Ensembl rs17850324, REVEL 0.36, MetaLR 0.20
- R127G (p.Arg127Gly), rs775065505, ClinGen CA1648541, ClinVar RCV002234997, ExAC rs775065505, REVEL 0.56, MetaLR 0.34, Uncertain significance
Public CALM3 analysis runs
- CALM3 analysis run — CALM3 (231 variants) — completed 2026-08-20