Sugi Variant

Sugi Variant/FOXP1

FOXP1 — 1076 ClinVar variants

All ClinVar germline FOXP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 317 flagged for review →

113 Pathogenic · 9 Pathogenic/Likely pathogenic · 76 Likely pathogenic · 56 Conflicting · 59 Benign · 27 Benign/Likely benign · 366 Likely benign · 370 Uncertain significance

Full FOXP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 317

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 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 35

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 221

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 221

Predictors split 57

The independent predictors disagree with each other — read with care.

All FOXP1 variants

Pathogenic 113

  • c.1653-2A>T Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg497Ter Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg503fs Multiple submitters Inborn genetic diseases
  • p.Arg503Ter Multiple submitters FOXP1-related disorders
  • p.Arg514Cys Multiple submitters FOXP1-related disorder
  • p.Arg525Ter Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg544Ter Multiple submitters intellectual disability
  • p.Gln150fs Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln177Ter Multiple submitters Inborn genetic diseases
  • p.Gln192fs Multiple submitters Inborn genetic diseases
  • p.Gln476Ter Multiple submitters intellectual disability
  • p.Gln542Ter Multiple submitters
  • p.Leu391fs Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Leu414fs Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Leu517Phe Multiple submitters Inborn genetic diseases
  • p.Lys393Ter Multiple submitters Inborn genetic diseases
  • p.Ser440Ter Multiple submitters
  • p.Tyr470Cys Multiple submitters
  • p.Tyr470Phe Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Val283fs Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1063-2A>G Single submitter Neurodevelopmental abnormality
  • c.1146+1G>T Single submitter
  • c.1147-1_1161dup Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1147-1G>A Single submitter
  • c.1348+1G>A Single submitter intellectual disability
  • c.1348+1G>C Single submitter autism
  • c.1349-5_1350del Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1428+2T>G Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1531-31_1531-15del Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1531-9_1534dup Single submitter Inborn genetic diseases
  • c.1652+1G>A Single submitter
  • c.1653-1G>A Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1653-2A>G Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1717_1722+5del Single submitter
  • c.1718_1722+8del Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1722+1G>T Single submitter Inborn genetic diseases
  • c.1889+1G>T Single submitter
  • c.869+1G>A Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.870-1G>C Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.870-2A>G Single submitter
  • c.975-2A>G Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.-11-2A>G Single submitter
  • p.Ala450= Single submitter intellectual disability
  • p.Ala450Thr Single submitter ⚠
  • p.Ala500fs Single submitter
  • p.Ala532fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ala572_Gln574delinsValAspTer Single submitter
  • p.Ala599delinsThrTer Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg465Thr Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Asn247fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Asn516_Leu517del Single submitter Inborn genetic diseases
  • p.Asn552fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Asn673fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Asp335fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Asp358fs Single submitter
  • p.Asp441fs Single submitter
  • p.Asp88delinsGluTer Single submitter Inborn genetic diseases
  • p.Gln162fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln167fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln171Ter Single submitter
  • p.Gln178Ter Single submitter
  • p.Gln187Ter Single submitter
  • p.Gln192Ter Single submitter
  • p.Gln194Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln200Ter Single submitter Inborn genetic diseases
  • p.Gln208Ter Single submitter isolated cerebellar hypoplasia/agenesis
  • p.Gln211Ter Single submitter
  • p.Gln221fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln280Ter Single submitter
  • p.Gln344fs Single submitter
  • p.Gln363Ter Single submitter
  • p.Gln381Ter Single submitter
  • p.Gln419Ter Single submitter Inborn genetic diseases
  • p.Gln72Ter Single submitter
  • p.Glu152fs Single submitter FOXP1-related disorders
  • p.Glu170Ter Single submitter
  • p.Glu480fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Glu483fs Single submitter FOXP1-related neurodevelopmental disorder
  • p.Gly165fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gly203fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.His163fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.His305fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ile474fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Leu488fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Lys325fs Single submitter
  • p.Lys442fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Phe523fs Single submitter Inborn genetic diseases
  • p.Pro407fs Single submitter
  • p.Pro413_Leu414insTer Single submitter
  • p.Pro553fs Single submitter
  • p.Ser276fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ser422fs Single submitter
  • p.Ser562fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Thr408fs Single submitter
  • p.Thr431fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Thr508fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Thr587fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Trp494Ter Single submitter
  • p.Tyr303Ter Single submitter
  • p.Tyr439Ter Single submitter
  • p.Tyr443Ter Single submitter
  • p.Tyr492Ter Single submitter
  • p.Tyr501Ter Single submitter
  • p.Val120_Leu121insTer Single submitter intellectual disability
  • p.Val316fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Val417fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Val445fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Val524fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1530+1G>T No assertion criteria intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.975-2A>C No assertion criteria intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln202Ter No assertion criteria intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ser518Asn No assertion criteria intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Trp310Ter No assertion criteria intellectual disability-severe speech delay-mild dysmorphism syndrome

Pathogenic/Likely pathogenic 9

  • c.1146+1G>A Multiple submitters Inborn genetic diseases
  • c.1426_1428+1del Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1652+5G>C Multiple submitters Inborn genetic diseases
  • p.Arg465Gly Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg497Pro Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg514His Multiple submitters FOXP1-related disorders
  • p.Arg525Gln Multiple submitters FOXP1-related disorders
  • p.Phe502Leu Multiple submitters Inborn genetic diseases
  • p.Val513Ala Multiple submitters Inborn genetic diseases

Likely pathogenic 76

  • c.1429-1G>A Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg544Gln Multiple submitters Inborn genetic diseases
  • p.Thr469Ile Multiple submitters intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1063-2485_1146+1457del Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1146+1G>C Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1146+4_1146+7del Single submitter FOXP1-related disorders
  • c.1147-2A>G Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1349-1G>A Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1429-13_1429-3del Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1429-1G>T Single submitter
  • c.1643_1652+3del Single submitter
  • c.1652+2T>C Single submitter FOXP1-related disorders
  • c.1653-1G>C Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1710_1722+2del Single submitter
  • c.1722+1G>A Single submitter
  • c.180+147del Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • c.1889+5G>A Single submitter
  • c.1889+5G>T Single submitter
  • c.282+2T>C Single submitter
  • c.511-6_511del Single submitter
  • c.870-2A>C Single submitter FOXP1-related disorder
  • p.Ala378fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ala398fs Single submitter FOXP1-related disorders
  • p.Ala512fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ala532Val Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg465delinsSerTer Single submitter FOXP1-related disorders
  • p.Arg514Pro Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Arg525Gly Single submitter
  • p.Asn516fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Asn528fs Single submitter intellectual disability
  • p.Asn558fs Single submitter
  • p.Asp334fs Single submitter neurodevelopmental disorder
  • p.Asp334His Single submitter intellectual disability
  • p.Asp451His Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Cys341Arg Single submitter
  • p.Gln105fs Single submitter
  • p.Gln162Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln172Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln401Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln476Pro Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gln574His Single submitter ⚠
  • p.Gln57Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Glu360fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Glu397Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Gly304Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.His368fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.His563fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ile478Ser Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Leu143fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Leu199Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Leu231_Trp232insTer Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Leu355Pro Single submitter
  • p.Leu517_Phe523del Single submitter FOXP1-related disorders
  • p.Leu517Arg Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Lys484fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Lys548fs Single submitter FOXP1-related disorders
  • p.Met223fs Single submitter FOXP1-related disorders
  • p.Met366Val Single submitter
  • p.Met577Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Phe523Leu Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Pro466Ala Single submitter Glabellar hemangioma
  • p.Pro466Ser Single submitter FOXP1-related disorders
  • p.Ser290Thr Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome ⚠
  • p.Ser387Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ser396Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Ser518fs Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Trp494_Phe495insTyrTrp Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Trp534Arg Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Trp534Ter Single submitter intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Tyr439fs Single submitter
  • c.1348+2T>C No assertion criteria autism
  • c.1428+1G>C No assertion criteria
  • c.1653-31_1653-26del No assertion criteria
  • p.Ala339Asp No assertion criteria
  • p.Pro466Leu No assertion criteria intellectual disability-severe speech delay-mild dysmorphism syndrome
  • p.Val423fs No assertion criteria intellectual disability-severe speech delay-mild dysmorphism syndrome

Conflicting classifications of pathogenicity 56

Benign 59

Benign/Likely benign 27

Likely benign 366

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 370

Showing the top 300 by review status; the full set is in the sitemap.