CPSF3 — 59 ClinVar variants

All ClinVar germline CPSF3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 47 flagged for review →

1 Pathogenic · 1 Likely pathogenic · 9 Likely benign · 48 Uncertain significance

Full CPSF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 47

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 lean, ClinVar uncertain 30

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

CPSF3 p.Ala147Val Uncertain significance Single submitter
CPSF3 p.Ala430Thr Uncertain significance Single submitter
CPSF3 p.Ala516Val Uncertain significance Single submitter
CPSF3 p.Ala6Ser Uncertain significance Single submitter
CPSF3 p.Arg215His Uncertain significance Single submitter
CPSF3 p.Arg613Thr Uncertain significance Single submitter
CPSF3 p.Asn645Ser Uncertain significance Single submitter
CPSF3 p.Asp40Asn Uncertain significance Single submitter
CPSF3 p.Gln515His Uncertain significance Single submitter
CPSF3 p.Glu654Gln Uncertain significance Single submitter
CPSF3 p.Glu657Asp Uncertain significance Single submitter
CPSF3 p.Gly658Glu Uncertain significance Single submitter
CPSF3 p.His608Asp Uncertain significance Single submitter
neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures
CPSF3 p.Ile167Thr Uncertain significance Single submitter
CPSF3 p.Ile202Thr Uncertain significance Single submitter
CPSF3 p.Ile29Thr Uncertain significance Single submitter
neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures
CPSF3 p.Ile354Thr Uncertain significance Single submitter
neurodevelopmental disorder with hypotonia, microcephaly, and seizures
CPSF3 p.Ile367Val Uncertain significance Single submitter
CPSF3 p.Ile616Phe Uncertain significance Single submitter
CPSF3 p.Leu431Pro Uncertain significance Single submitter
CPSF3 p.Leu68Ser Uncertain significance Single submitter
CPSF3 p.Phe140Ser Uncertain significance Single submitter
CPSF3 p.Pro371Ser Uncertain significance Single submitter
CPSF3 p.Pro571Leu Uncertain significance Single submitter
CPSF3 p.Ser387Phe Uncertain significance Single submitter
CPSF3 p.Thr402Ile Uncertain significance Single submitter
CPSF3 p.Thr520Ser Uncertain significance Single submitter
CPSF3 p.Val388Ile Uncertain significance Single submitter
CPSF3 p.Val601Ile Uncertain significance Single submitter
CPSF3 p.Arg218Gln Uncertain significance No assertion criteria
neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures

Predictors split 17

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

All CPSF3 variants

Pathogenic 1

p.Gly468Glu No assertion criteria neurodevelopmental disorder with hypotonia, microcephaly, and seizures

Likely pathogenic 1

c.761-1G>T No assertion criteria HP:0001252; HP:0001776; HP:0000252; HP:0001270; HP:0000592

Likely benign 9

c.-97G>T Single submitter
p.Arg294= Single submitter
p.Asn115= Single submitter
p.Gln513= Single submitter
p.Glu670= Single submitter
p.Leu665= Single submitter
p.Lys473Arg Single submitter
p.Ser334= Single submitter
p.Ser482= Single submitter

Uncertain significance 48

p.Ile354Met Multiple submitters neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures ⚠
c.51-2165C>G Single submitter neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures
p.Ala147Val Single submitter ⚠
p.Ala190Val Single submitter ⚠
p.Ala430Thr Single submitter ⚠
p.Ala516Val Single submitter ⚠
p.Ala6Ser Single submitter ⚠
p.Arg215His Single submitter ⚠
p.Arg480Gln Single submitter ⚠
p.Arg480Trp Single submitter ⚠
p.Arg613Thr Single submitter ⚠
p.Arg651Trp Single submitter ⚠
p.Asn645Ser Single submitter ⚠
p.Asp40Asn Single submitter ⚠
p.Gln400His Single submitter ⚠
p.Gln515His Single submitter ⚠
p.Glu654Gln Single submitter ⚠
p.Glu657Asp Single submitter ⚠
p.Gly641Arg Single submitter ⚠
p.Gly658Glu Single submitter ⚠
p.His608Asp Single submitter neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures ⚠
p.Ile167Thr Single submitter ⚠
p.Ile202Thr Single submitter ⚠
p.Ile202Val Single submitter ⚠
p.Ile229Val Single submitter ⚠
p.Ile29Thr Single submitter neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures ⚠
p.Ile354Thr Single submitter neurodevelopmental disorder with hypotonia, microcephaly, and seizures ⚠
p.Ile367Val Single submitter ⚠
p.Ile616Phe Single submitter ⚠
p.Leu431Pro Single submitter ⚠
p.Leu68Ser Single submitter ⚠
p.Lys295Glu Single submitter ⚠
p.Phe140Ser Single submitter ⚠
p.Pro371Ser Single submitter ⚠
p.Pro571Leu Single submitter ⚠
p.Pro571Thr Single submitter ⚠
p.Ser387Phe Single submitter ⚠
p.Thr346Ile Single submitter ⚠
p.Thr402Ile Single submitter ⚠
p.Thr520Ser Single submitter ⚠
p.Thr555Ile Single submitter ⚠
p.Tyr528Cys Single submitter ⚠
p.Val159Ile Single submitter ⚠
p.Val388Ile Single submitter ⚠
p.Val601Ile Single submitter ⚠
p.Val627Gly Single submitter ⚠
p.Val637Ile Single submitter ⚠
p.Arg218Gln No assertion criteria neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures ⚠