NKAP — 82 ClinVar variants
All ClinVar germline NKAP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 53 flagged for review →
2 Pathogenic · 2 Pathogenic/Likely pathogenic · 4 Conflicting · 5 Benign · 16 Likely benign · 53 Uncertain significance
Full NKAP gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 53
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 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
NKAP p.Arg330Cys
Conflicting
Single submitter
Inborn genetic diseases
- NKAP p.Arg360Cys Conflicting Single submitter
Predictors lean, ClinVar uncertain 33
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
NKAP p.Glu271Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
NKAP p.Ile90Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
NKAP p.Lys184Glu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
NKAP p.Pro332Ser
Uncertain significance
Multiple submitters
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
-
NKAP p.Val99Ile
Uncertain significance
Multiple submitters
NKAP-related disorder
- NKAP p.Arg196Thr Uncertain significance Single submitter
- NKAP p.Arg22Pro Uncertain significance Single submitter
-
NKAP p.Arg361Gln
Uncertain significance
Single submitter
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
-
NKAP p.Arg43His
Uncertain significance
Single submitter
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
-
NKAP p.Arg43Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- NKAP p.Arg8Cys Uncertain significance Single submitter
-
NKAP p.Asp225Glu
Uncertain significance
Single submitter
Inborn genetic diseases
- NKAP p.Cys47Tyr Uncertain significance Single submitter
-
NKAP p.Glu167Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- NKAP p.Gly316Ala Uncertain significance Single submitter
-
NKAP p.Gly6Cys
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Lys184Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Lys267Glu
Uncertain significance
Single submitter
Inborn genetic diseases
- NKAP p.Lys29Arg Uncertain significance Single submitter
- NKAP p.Pro107Ser Uncertain significance Single submitter
-
NKAP p.Pro115Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Pro115Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Pro168Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Pro84Ser
Uncertain significance
Single submitter
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
-
NKAP p.Ser116Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- NKAP p.Ser171Ile Uncertain significance Single submitter
- NKAP p.Ser71Thr Uncertain significance Single submitter
-
NKAP p.Ser96Phe
Uncertain significance
Single submitter
Inborn genetic diseases
- NKAP p.Thr173Ile Uncertain significance Single submitter
- NKAP p.Thr282Ile Uncertain significance Single submitter
-
NKAP p.Tyr324Cys
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Asp218Tyr
Uncertain significance
No assertion criteria
NKAP-related disorder
-
NKAP p.Pro37Leu
Uncertain significance
No assertion criteria
NKAP-related disorder
Predictors split 18
The independent predictors disagree with each other — read with care.
-
NKAP p.Lys256Asn
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
NKAP p.Arg360His
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Arg402Gln
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Arg41Cys
Conflicting
Single submitter
Inborn genetic diseases
-
NKAP p.Glu124Lys
Uncertain significance
Single submitter
developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy
- NKAP p.Glu139Lys Uncertain significance Single submitter
-
NKAP p.Glu159Ala
Uncertain significance
Single submitter
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
-
NKAP p.Glu343Asp
Uncertain significance
Single submitter
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- NKAP p.Lys199Ile Uncertain significance Single submitter
-
NKAP p.Ser17Trp
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Ser213Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Ser224Gly
Likely benign
Single submitter
Inborn genetic diseases
-
NKAP p.Ser265Asn
Likely benign
Single submitter
Inborn genetic diseases
-
NKAP p.Ser346Leu
Uncertain significance
Single submitter
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
-
NKAP p.Ser46Phe
Uncertain significance
Single submitter
Inborn genetic diseases
-
NKAP p.Ser48Cys
Uncertain significance
Single submitter
intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
-
NKAP p.Ser48Phe
Conflicting
Single submitter
Inborn genetic diseases
-
NKAP p.Ser50Phe
Uncertain significance
Single submitter
Inborn genetic diseases
All NKAP variants
Pathogenic 2
- p.Met321Val Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- p.Ile337Thr No assertion criteria intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
Pathogenic/Likely pathogenic 2
- p.Arg330His Multiple submitters intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- p.Arg333Gln Multiple submitters intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
Conflicting classifications of pathogenicity 4
- p.Arg330Cys Single submitter Inborn genetic diseases ⚠
- p.Arg360Cys Single submitter ⚠
- p.Arg41Cys Single submitter Inborn genetic diseases ⚠
- p.Ser48Phe Single submitter Inborn genetic diseases ⚠
Benign 5
- c.538+8T>A Multiple submitters intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- c.539-17A>T Multiple submitters intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- c.923+6C>T Multiple submitters intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- p.Pro107= Single submitter
- p.Ser202del Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
Likely benign 16
- c.538+9A>T Single submitter
- c.673+18A>G Single submitter
- c.673+7A>G Single submitter
- p.Arg122Lys Single submitter Inborn genetic diseases
- p.Arg196Lys Single submitter Inborn genetic diseases
- p.Asp111His Single submitter Inborn genetic diseases
- p.Leu313= Single submitter
- p.Lys185del Single submitter
- p.Lys247= Single submitter
- p.Pro287= Single submitter
- p.Ser224Gly Single submitter Inborn genetic diseases ⚠
- p.Ser265Asn Single submitter Inborn genetic diseases ⚠
- p.Ser31Gly Single submitter Inborn genetic diseases
- p.Tyr100Cys Single submitter
- p.Val145= Single submitter
- p.Ala284Ser No assertion criteria NKAP-related disorder
Uncertain significance 53
- p.Glu271Val Multiple submitters Inborn genetic diseases ⚠
- p.Ile90Val Multiple submitters Inborn genetic diseases ⚠
- p.Lys184Glu Multiple submitters Inborn genetic diseases ⚠
- p.Lys256Asn Multiple submitters Inborn genetic diseases ⚠
- p.Pro332Ser Multiple submitters intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Val99Ile Multiple submitters NKAP-related disorder ⚠
- c.1073+1672_1074-1701del Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- p.74SR[3] Single submitter
- p.Arg196Thr Single submitter ⚠
- p.Arg22Pro Single submitter ⚠
- p.Arg360His Single submitter Inborn genetic diseases ⚠
- p.Arg361Gln Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Arg402Gln Single submitter Inborn genetic diseases ⚠
- p.Arg43His Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Arg43Leu Single submitter Inborn genetic diseases ⚠
- p.Arg8Cys Single submitter ⚠
- p.Asp225Glu Single submitter Inborn genetic diseases ⚠
- p.Cys47Tyr Single submitter ⚠
- p.Glu124Lys Single submitter developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy ⚠
- p.Glu139Lys Single submitter ⚠
- p.Glu159Ala Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Glu167Gly Single submitter Inborn genetic diseases ⚠
- p.Glu343Asp Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Gly316Ala Single submitter ⚠
- p.Gly6Cys Single submitter Inborn genetic diseases ⚠
- p.Lys184Arg Single submitter Inborn genetic diseases ⚠
- p.Lys199Ile Single submitter ⚠
- p.Lys237_Lys238del Single submitter
- p.Lys243del Single submitter
- p.Lys267Glu Single submitter Inborn genetic diseases ⚠
- p.Lys29Arg Single submitter ⚠
- p.Pro107Ser Single submitter ⚠
- p.Pro115Leu Single submitter Inborn genetic diseases ⚠
- p.Pro115Ser Single submitter Inborn genetic diseases ⚠
- p.Pro168Leu Single submitter Inborn genetic diseases ⚠
- p.Pro84Ser Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Ser116Ile Single submitter Inborn genetic diseases ⚠
- p.Ser171Ile Single submitter ⚠
- p.Ser17Trp Single submitter Inborn genetic diseases ⚠
- p.Ser213Arg Single submitter Inborn genetic diseases ⚠
- p.Ser346Leu Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Ser46Phe Single submitter Inborn genetic diseases ⚠
- p.Ser48Cys Single submitter intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type ⚠
- p.Ser50Phe Single submitter Inborn genetic diseases ⚠
- p.Ser71Thr Single submitter ⚠
- p.Ser96Phe Single submitter Inborn genetic diseases ⚠
- p.Ter416AspextTer? Single submitter
- p.Thr173Ile Single submitter ⚠
- p.Thr282Ile Single submitter ⚠
- p.Tyr324Cys Single submitter Inborn genetic diseases ⚠
- c.924-10_*10dup No assertion criteria intellectual developmental disorder, X-linked, syndromic, Hackmann-Di Donato type
- p.Asp218Tyr No assertion criteria NKAP-related disorder ⚠
- p.Pro37Leu No assertion criteria NKAP-related disorder ⚠