PLCD1 — 237 ClinVar variants
All ClinVar germline PLCD1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 150 flagged for review →
4 Pathogenic · 1 Pathogenic/Likely pathogenic · 6 Likely pathogenic · 1 Conflicting · 25 Benign · 3 Benign/Likely benign · 36 Likely benign · 161 Uncertain significance
Full PLCD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 150
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 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
PLCD1 p.Ala553Thr
Conflicting
No assertion criteria
PLCD1-related disorder
Predictors lean, ClinVar uncertain 121
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
PLCD1 p.Arg138His
Uncertain significance
Multiple submitters
nonsyndromic congenital nail disorder 3
-
PLCD1 p.Arg476His
Uncertain significance
Multiple submitters
nonsyndromic congenital nail disorder 3
-
PLCD1 p.Arg60Gln
Uncertain significance
Multiple submitters
nonsyndromic congenital nail disorder 3
- PLCD1 p.Ser650Ala Uncertain significance Multiple submitters
- PLCD1 p.Ala118Thr Uncertain significance Single submitter
- PLCD1 p.Ala219Thr Uncertain significance Single submitter
- PLCD1 p.Ala21Val Uncertain significance Single submitter
- PLCD1 p.Ala222Ser Uncertain significance Single submitter
- PLCD1 p.Ala222Val Uncertain significance Single submitter
- PLCD1 p.Ala249Val Uncertain significance Single submitter
- PLCD1 p.Ala286Thr Uncertain significance Single submitter
- PLCD1 p.Ala380Thr Uncertain significance Single submitter
- PLCD1 p.Ala380Val Uncertain significance Single submitter
-
PLCD1 p.Ala402Val
Uncertain significance
Single submitter
nonsyndromic congenital nail disorder 3
- PLCD1 p.Ala456Thr Uncertain significance Single submitter
- PLCD1 p.Ala466Gly Uncertain significance Single submitter
- PLCD1 p.Ala606Thr Uncertain significance Single submitter
- PLCD1 p.Ala619Thr Uncertain significance Single submitter
- PLCD1 p.Ala627Ser Uncertain significance Single submitter
- PLCD1 p.Arg150Leu Uncertain significance Single submitter
- PLCD1 p.Arg186Trp Uncertain significance Single submitter
- PLCD1 p.Arg211Gln Uncertain significance Single submitter
-
PLCD1 p.Arg211Trp
Uncertain significance
Single submitter
Primary degenerative dementia of the Alzheimer type, presenile onset
- PLCD1 p.Arg216His Uncertain significance Single submitter
- PLCD1 p.Arg242Gln Uncertain significance Single submitter
- PLCD1 p.Arg242Gly Uncertain significance Single submitter
- PLCD1 p.Arg268Gln Uncertain significance Single submitter
- PLCD1 p.Arg292His Uncertain significance Single submitter
- PLCD1 p.Arg293His Uncertain significance Single submitter
- PLCD1 p.Arg38Lys Uncertain significance Single submitter
- PLCD1 p.Arg403Gln Uncertain significance Single submitter
- PLCD1 p.Arg476Cys Uncertain significance Single submitter
- PLCD1 p.Arg541His Uncertain significance Single submitter
- PLCD1 p.Arg592Cys Uncertain significance Single submitter
- PLCD1 p.Arg628Gln Uncertain significance Single submitter
- PLCD1 p.Arg630Gln Uncertain significance Single submitter
- PLCD1 p.Arg670Cys Uncertain significance Single submitter
- PLCD1 p.Arg670His Uncertain significance Single submitter
- PLCD1 p.Arg701Cys Uncertain significance Single submitter
- PLCD1 p.Arg95Cys Uncertain significance Single submitter
- PLCD1 p.Arg95His Uncertain significance Single submitter
- PLCD1 p.Asn158Asp Uncertain significance Single submitter
- PLCD1 p.Asn158Ser Uncertain significance Single submitter
- PLCD1 p.Asn578Ser Uncertain significance Single submitter
- PLCD1 p.Asn612Lys Uncertain significance Single submitter
- PLCD1 p.Asn632His Uncertain significance Single submitter
- PLCD1 p.Asn632Lys Uncertain significance Single submitter
- PLCD1 p.Asp136Ala Uncertain significance Single submitter
- PLCD1 p.Asp194Gly Uncertain significance Single submitter
- PLCD1 p.Asp198Asn Uncertain significance Single submitter
-
PLCD1 p.Cys339Phe
Uncertain significance
Single submitter
nonsyndromic congenital nail disorder 3
- PLCD1 p.Gln139Glu Uncertain significance Single submitter
- PLCD1 p.Gln192Arg Uncertain significance Single submitter
- PLCD1 p.Gln671His Uncertain significance Single submitter
- PLCD1 p.Gln728Lys Uncertain significance Single submitter
- PLCD1 p.Gln742Arg Uncertain significance Single submitter
- PLCD1 p.Glu202Lys Uncertain significance Single submitter
- PLCD1 p.Glu244Ala Uncertain significance Single submitter
- PLCD1 p.Glu262Lys Uncertain significance Single submitter
- PLCD1 p.Glu455Lys Uncertain significance Single submitter
- PLCD1 p.Glu63Asp Uncertain significance Single submitter
- PLCD1 p.Glu70Lys Uncertain significance Single submitter
- PLCD1 p.Gly223Asp Uncertain significance Single submitter
- PLCD1 p.Gly284Ser Uncertain significance Single submitter
- PLCD1 p.Gly322Arg Uncertain significance Single submitter
- PLCD1 p.Gly336Ala Uncertain significance Single submitter
- PLCD1 p.Gly347Arg Uncertain significance Single submitter
- PLCD1 p.Gly357Ser Uncertain significance Single submitter
- PLCD1 p.Gly450Glu Uncertain significance Single submitter
- PLCD1 p.Gly453Ser Uncertain significance Single submitter
- PLCD1 p.Gly505Trp Uncertain significance Single submitter
- PLCD1 p.Gly538Arg Uncertain significance Single submitter
- PLCD1 p.Gly597Arg Uncertain significance Single submitter
- PLCD1 p.Gly740Arg Uncertain significance Single submitter
- PLCD1 p.His11Tyr Uncertain significance Single submitter
- PLCD1 p.His120Arg Uncertain significance Single submitter
- PLCD1 p.His146Gln Uncertain significance Single submitter
- PLCD1 p.His503Pro Uncertain significance Single submitter
-
PLCD1 p.Ile373Thr
Uncertain significance
Single submitter
nonsyndromic congenital nail disorder 3
- PLCD1 p.Ile716Val Uncertain significance Single submitter
- PLCD1 p.Ile721Val Uncertain significance Single submitter
- PLCD1 p.Leu302His Uncertain significance Single submitter
- PLCD1 p.Leu315Gln Uncertain significance Single submitter
- PLCD1 p.Leu342Arg Uncertain significance Single submitter
- PLCD1 p.Leu445Phe Uncertain significance Single submitter
- PLCD1 p.Leu488Ile Uncertain significance Single submitter
- PLCD1 p.Leu641Gln Uncertain significance Single submitter
- PLCD1 p.Leu723Val Uncertain significance Single submitter
- PLCD1 p.Lys127Arg Uncertain significance Single submitter
- PLCD1 p.Lys170Thr Uncertain significance Single submitter
- PLCD1 p.Lys206Arg Uncertain significance Single submitter
- PLCD1 p.Lys438Asn Uncertain significance Single submitter
- PLCD1 p.Lys712Gln Uncertain significance Single submitter
- PLCD1 p.Lys738Arg Uncertain significance Single submitter
- PLCD1 p.Met135Lys Uncertain significance Single submitter
- PLCD1 p.Met135Val Uncertain significance Single submitter
- PLCD1 p.Met160Arg Uncertain significance Single submitter
- PLCD1 p.Met401Thr Uncertain significance Single submitter
- PLCD1 p.Phe236Leu Uncertain significance Single submitter
- PLCD1 p.Phe702Ser Uncertain significance Single submitter
- PLCD1 p.Pro448Ser Uncertain significance Single submitter
- PLCD1 p.Pro481Thr Uncertain significance Single submitter
- PLCD1 p.Pro513Arg Uncertain significance Single submitter
- PLCD1 p.Pro552Leu Uncertain significance Single submitter
- PLCD1 p.Pro682Ser Uncertain significance Single submitter
- PLCD1 p.Ser147Phe Uncertain significance Single submitter
- PLCD1 p.Ser281Leu Uncertain significance Single submitter
- PLCD1 p.Ser501Asn Uncertain significance Single submitter
- PLCD1 p.Ser508Ala Uncertain significance Single submitter
- PLCD1 p.Ser563Gly Uncertain significance Single submitter
- PLCD1 p.Ser637Leu Uncertain significance Single submitter
- PLCD1 p.Ser710Thr Uncertain significance Single submitter
- PLCD1 p.Thr193Ile Uncertain significance Single submitter
- PLCD1 p.Thr235Met Uncertain significance Single submitter
- PLCD1 p.Thr686Met Uncertain significance Single submitter
- PLCD1 p.Thr9Ser Uncertain significance Single submitter
- PLCD1 p.Tyr180Phe Uncertain significance Single submitter
- PLCD1 p.Tyr358Cys Uncertain significance Single submitter
- PLCD1 p.Val544Met Uncertain significance Single submitter
- PLCD1 p.Val663Met Uncertain significance Single submitter
- PLCD1 p.Thr217Asn Uncertain significance No assertion criteria
Predictors split 27
The independent predictors disagree with each other — read with care.
- PLCD1 p.Pro417Arg Uncertain significance Multiple submitters
- PLCD1 p.Ala112Thr Uncertain significance Single submitter
- PLCD1 p.Arg105Cys Uncertain significance Single submitter
- PLCD1 p.Arg242Trp Uncertain significance Single submitter
- PLCD1 p.Arg331Trp Uncertain significance Single submitter
- PLCD1 p.Arg403Trp Uncertain significance Single submitter
- PLCD1 p.Arg40Cys Uncertain significance Single submitter
- PLCD1 p.Arg40His Uncertain significance Single submitter
- PLCD1 p.Arg56Cys Uncertain significance Single submitter
- PLCD1 p.Arg60Trp Uncertain significance Single submitter
- PLCD1 p.Arg630Trp Uncertain significance Single submitter
- PLCD1 p.Asp215Asn Uncertain significance Single submitter
- PLCD1 p.Cys499Ser Uncertain significance Single submitter
- PLCD1 p.Glu220Lys Uncertain significance Single submitter
- PLCD1 p.Glu467Lys Uncertain significance Single submitter
-
PLCD1 p.Gly536Arg
Uncertain significance
Single submitter
nonsyndromic congenital nail disorder 3
- PLCD1 p.His406Pro Uncertain significance Single submitter
- PLCD1 p.Ile201Ser Uncertain significance Single submitter
- PLCD1 p.Pro382Leu Uncertain significance Single submitter
- PLCD1 p.Pro617Ser Likely benign Single submitter
- PLCD1 p.Ser229Leu Uncertain significance Single submitter
- PLCD1 p.Ser725Arg Uncertain significance Single submitter
- PLCD1 p.Trp625Arg Uncertain significance Single submitter
- PLCD1 p.Tyr355Cys Uncertain significance Single submitter
- PLCD1 p.Tyr518Cys Uncertain significance Single submitter
- PLCD1 p.Val400Met Uncertain significance Single submitter
-
PLCD1 p.Glu462Lys
Uncertain significance
No assertion criteria
PLCD1-related disorder
All PLCD1 variants
Pathogenic 4
- p.Gln580Ter Single submitter
- c.1724-5_1728del No assertion criteria nonsyndromic congenital nail disorder 3
- p.Arg416Ter No assertion criteria nonsyndromic congenital nail disorder 3
- p.Cys188Arg No assertion criteria nonsyndromic congenital nail disorder 3
Pathogenic/Likely pathogenic 1
- p.Arg530Ter Multiple submitters nonsyndromic congenital nail disorder 3
Likely pathogenic 6
- p.Arg331Gln Single submitter ⚠
- p.Asn612fs Single submitter nonsyndromic congenital nail disorder 3
- p.Gln533Ter Single submitter nonsyndromic congenital nail disorder 3
- p.Gln622Ter Single submitter nonsyndromic congenital nail disorder 3
- p.Met495fs Single submitter PLCD1-related disorder
- p.Ile386fs No assertion criteria PLCD1-related disorder
Conflicting classifications of pathogenicity 1
- p.Ala553Thr No assertion criteria PLCD1-related disorder ⚠
Benign 25
- c.1607-42C>T Multiple submitters
- c.1724-186C>G Multiple submitters
- c.1724-32C>T Multiple submitters
- c.200-175C>A Multiple submitters
- c.200-257T>C Multiple submitters
- c.200-274C>G Multiple submitters
- c.200-31C>G Multiple submitters
- c.428+84T>C Multiple submitters
- c.429-42A>G Multiple submitters
- c.790+92C>G Multiple submitters
- p.Ala245= Multiple submitters
- p.Arg257His Multiple submitters
- p.Arg293Cys Multiple submitters
- p.Arg618= Multiple submitters
- p.Asp231Asn Multiple submitters
- p.Asp461= Multiple submitters
- p.Pro301= Multiple submitters
- c.199+139T>C Single submitter
- c.34+257A>T Single submitter
- c.429-159_429-158insTAACGGGACG Single submitter
- c.790+300dup Single submitter
- c.*234del Single submitter
- p.Ala222= Single submitter
- p.Gly299Ser Single submitter
- p.Ser460Leu No assertion criteria PLCD1-related disorder
Benign/Likely benign 3
Likely benign 36
- p.Ala290= Multiple submitters
- p.Asn543= Multiple submitters
- c.1447-12C>T Single submitter
- c.1724-5T>C Single submitter
- c.1902+19G>A Single submitter
- c.35-4000A>G Single submitter
- p.Ala266= Single submitter
- p.Ala266Val Single submitter
- p.Ala377= Single submitter
- p.Arg416Gln Single submitter
- p.Arg618Cys Single submitter
- p.Arg80His Single submitter
- p.Asn647Ser Single submitter
- p.Asp198= Single submitter
- p.Asp283= Single submitter
- p.Asp494= Single submitter
- p.Gly638= Single submitter
- p.His126Arg Single submitter
- p.His190Arg Single submitter
- p.Ile353Val Single submitter
- p.Ile550= Single submitter
- p.Ile700Val Single submitter
- p.Pro564= Single submitter
- p.Pro617Ser Single submitter ⚠
- p.Ser3= Single submitter
- p.Ser34= Single submitter
- p.Ser664Gly Single submitter
- p.Thr313= Single submitter
- c.429-5C>T No assertion criteria PLCD1-related disorder
- c.993-4G>A No assertion criteria PLCD1-related disorder
- c.993-5C>T No assertion criteria PLCD1-related disorder
- p.Ala249= No assertion criteria PLCD1-related disorder
- p.His546= No assertion criteria PLCD1-related disorder
- p.Lys49= No assertion criteria PLCD1-related disorder
- p.Ser281= No assertion criteria PLCD1-related disorder
- p.Ser548= No assertion criteria PLCD1-related disorder
Uncertain significance 161
- p.Arg138His Multiple submitters nonsyndromic congenital nail disorder 3 ⚠
- p.Arg476His Multiple submitters nonsyndromic congenital nail disorder 3 ⚠
- p.Arg60Gln Multiple submitters nonsyndromic congenital nail disorder 3 ⚠
- p.Pro417Arg Multiple submitters ⚠
- p.Ser650Ala Multiple submitters ⚠
- c.1137+5G>C Single submitter nonsyndromic congenital nail disorder 3
- c.35-3988C>G Single submitter
- c.35-3998T>G Single submitter
- c.35-4008C>T Single submitter
- c.35-4017T>G Single submitter
- c.35-4025G>C Single submitter
- c.35-4056G>A Single submitter
- c.35-4058C>G Single submitter
- c.35-4069G>A Single submitter
- p.Ala112Thr Single submitter ⚠
- p.Ala118Thr Single submitter ⚠
- p.Ala219Thr Single submitter ⚠
- p.Ala21Val Single submitter ⚠
- p.Ala222Ser Single submitter ⚠
- p.Ala222Val Single submitter ⚠
- p.Ala249Val Single submitter ⚠
- p.Ala286Thr Single submitter ⚠
- p.Ala380Thr Single submitter ⚠
- p.Ala380Val Single submitter ⚠
- p.Ala402Val Single submitter nonsyndromic congenital nail disorder 3 ⚠
- p.Ala456Thr Single submitter ⚠
- p.Ala466Gly Single submitter ⚠
- p.Ala606Thr Single submitter ⚠
- p.Ala619Thr Single submitter ⚠
- p.Ala627Ser Single submitter ⚠
- p.Arg105Cys Single submitter ⚠
- p.Arg150Leu Single submitter ⚠
- p.Arg186Trp Single submitter ⚠
- p.Arg211Gln Single submitter ⚠
- p.Arg211Trp Single submitter Primary degenerative dementia of the Alzheimer type, presenile onset ⚠
- p.Arg216His Single submitter ⚠
- p.Arg242Gln Single submitter ⚠
- p.Arg242Gly Single submitter ⚠
- p.Arg242Trp Single submitter ⚠
- p.Arg268Gln Single submitter ⚠
- p.Arg292His Single submitter ⚠
- p.Arg293His Single submitter ⚠
- p.Arg331Trp Single submitter ⚠
- p.Arg38Lys Single submitter ⚠
- p.Arg403Gln Single submitter ⚠
- p.Arg403Trp Single submitter ⚠
- p.Arg40Cys Single submitter ⚠
- p.Arg40His Single submitter ⚠
- p.Arg476Cys Single submitter ⚠
- p.Arg541His Single submitter ⚠
- p.Arg56Cys Single submitter ⚠
- p.Arg592Cys Single submitter ⚠
- p.Arg60Trp Single submitter ⚠
- p.Arg628Gln Single submitter ⚠
- p.Arg630Gln Single submitter ⚠
- p.Arg630Trp Single submitter ⚠
- p.Arg670Cys Single submitter ⚠
- p.Arg670His Single submitter ⚠
- p.Arg701Cys Single submitter ⚠
- p.Arg701His Single submitter
- p.Arg95Cys Single submitter ⚠
- p.Arg95His Single submitter ⚠
- p.Asn158Asp Single submitter ⚠
- p.Asn158Ser Single submitter ⚠
- p.Asn578Ser Single submitter ⚠
- p.Asn612Lys Single submitter ⚠
- p.Asn632His Single submitter ⚠
- p.Asn632Lys Single submitter ⚠
- p.Asp136Ala Single submitter ⚠
- p.Asp194Gly Single submitter ⚠
- p.Asp198Asn Single submitter ⚠
- p.Asp215Asn Single submitter ⚠
- p.Cys339Phe Single submitter nonsyndromic congenital nail disorder 3 ⚠
- p.Cys499Ser Single submitter ⚠
- p.Gln139Glu Single submitter ⚠
- p.Gln192Arg Single submitter ⚠
- p.Gln671His Single submitter ⚠
- p.Gln728Lys Single submitter ⚠
- p.Gln742Arg Single submitter ⚠
- p.Glu202Lys Single submitter ⚠
- p.Glu220Lys Single submitter ⚠
- p.Glu244Ala Single submitter ⚠
- p.Glu262Lys Single submitter ⚠
- p.Glu455Lys Single submitter ⚠
- p.Glu467Lys Single submitter ⚠
- p.Glu63Asp Single submitter ⚠
- p.Glu70Lys Single submitter ⚠
- p.Gly223Asp Single submitter ⚠
- p.Gly284Ser Single submitter ⚠
- p.Gly322Arg Single submitter ⚠
- p.Gly336Ala Single submitter ⚠
- p.Gly347Arg Single submitter ⚠
- p.Gly357Ser Single submitter ⚠
- p.Gly450Glu Single submitter ⚠
- p.Gly453Ser Single submitter ⚠
- p.Gly505Trp Single submitter ⚠
- p.Gly536Arg Single submitter nonsyndromic congenital nail disorder 3 ⚠
- p.Gly538Arg Single submitter ⚠
- p.Gly597Arg Single submitter ⚠
- p.Gly740Arg Single submitter ⚠
- p.His11Tyr Single submitter ⚠
- p.His120Arg Single submitter ⚠
- p.His146Gln Single submitter ⚠
- p.His291Pro Single submitter
- p.His406Pro Single submitter ⚠
- p.His503Pro Single submitter ⚠
- p.Ile201Ser Single submitter ⚠
- p.Ile373Thr Single submitter nonsyndromic congenital nail disorder 3 ⚠
- p.Ile716Val Single submitter ⚠
- p.Ile721Val Single submitter ⚠
- p.Leu302His Single submitter ⚠
- p.Leu315Gln Single submitter ⚠
- p.Leu342Arg Single submitter ⚠
- p.Leu445Phe Single submitter ⚠
- p.Leu488Ile Single submitter ⚠
- p.Leu641Gln Single submitter ⚠
- p.Leu723Val Single submitter ⚠
- p.Lys127Arg Single submitter ⚠
- p.Lys170Thr Single submitter ⚠
- p.Lys206Arg Single submitter ⚠
- p.Lys438Asn Single submitter ⚠
- p.Lys712Gln Single submitter ⚠
- p.Lys738Arg Single submitter ⚠
- p.Met135Lys Single submitter ⚠
- p.Met135Val Single submitter ⚠
- p.Met160Arg Single submitter ⚠
- p.Met401Thr Single submitter ⚠
- p.Phe236Leu Single submitter ⚠
- p.Phe702Ser Single submitter ⚠
- p.Pro382Leu Single submitter ⚠
- p.Pro448Ser Single submitter ⚠
- p.Pro481Thr Single submitter ⚠
- p.Pro513Arg Single submitter ⚠
- p.Pro552Leu Single submitter ⚠
- p.Pro682Ser Single submitter ⚠
- p.Ser147Phe Single submitter ⚠
- p.Ser229Leu Single submitter ⚠
- p.Ser281Leu Single submitter ⚠
- p.Ser362Ala Single submitter
- p.Ser501Asn Single submitter ⚠
- p.Ser508Ala Single submitter ⚠
- p.Ser563Gly Single submitter ⚠
- p.Ser637Leu Single submitter ⚠
- p.Ser710Thr Single submitter ⚠
- p.Ser725Arg Single submitter ⚠
- p.Thr193Ile Single submitter ⚠
- p.Thr235Met Single submitter ⚠
- p.Thr686Met Single submitter ⚠
- p.Thr9Ser Single submitter ⚠
- p.Trp625Arg Single submitter ⚠
- p.Tyr180Phe Single submitter ⚠
- p.Tyr355Cys Single submitter ⚠
- p.Tyr358Cys Single submitter ⚠
- p.Tyr518Cys Single submitter ⚠
- p.Val294Ala Single submitter
- p.Val400Met Single submitter ⚠
- p.Val544Met Single submitter ⚠
- p.Val663Met Single submitter ⚠
- p.Glu226_Val230del No assertion criteria
- p.Glu462Lys No assertion criteria PLCD1-related disorder ⚠
- p.Thr217Asn No assertion criteria ⚠