MCFD2 — 164 ClinVar variants

All ClinVar germline MCFD2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 31 flagged for review →

6 Pathogenic · 6 Likely pathogenic · 2 Conflicting · 39 Benign · 11 Likely benign · 100 Uncertain significance

Full MCFD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 31

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.

MCFD2 p.Leu16Pro Likely pathogenic Single submitter
factor 5 and Factor VIII, combined deficiency of, 2

Predictors lean, ClinVar uncertain 25

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

Predictors split 5

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

MCFD2 p.Met79Thr Uncertain significance Multiple submitters
factor 5 and Factor VIII, combined deficiency of, 2
MCFD2 p.Ala139Thr Uncertain significance Single submitter
MCFD2 p.Gln73Glu Uncertain significance Single submitter
MCFD2 p.His101Tyr Uncertain significance Single submitter
MCFD2 p.Asp122Asn Likely pathogenic No assertion criteria
Abnormal bleeding

All MCFD2 variants

Pathogenic 6

c.309+1G>A No assertion criteria factor 5 and Factor VIII, combined deficiency of, 2
p.Asp129Glu No assertion criteria factor 5 and Factor VIII, combined deficiency of, 2
p.Asp81Tyr No assertion criteria factor 5 and Factor VIII, combined deficiency of, 2
p.Asp83fs No assertion criteria factor 5 and Factor VIII, combined deficiency of, 2
p.Asp89fs No assertion criteria factor 5 and Factor VIII, combined deficiency of, 2
p.Ile136Thr No assertion criteria factor 5 and Factor VIII, combined deficiency of, 2

Likely pathogenic 6

c.149+5G>A Multiple submitters factor V and factor VIII, combined deficiency of, type 1
p.Asp127fs Single submitter factor V and factor VIII, combined deficiency of, type 1
p.Gln35fs Single submitter factor 5 and Factor VIII, combined deficiency of, 2
p.Leu16Pro Single submitter factor 5 and Factor VIII, combined deficiency of, 2 ⚠
c.-6-1668_*2631del No assertion criteria Reduced quantity of Von Willebrand factor
p.Asp122Asn No assertion criteria Abnormal bleeding ⚠

Conflicting classifications of pathogenicity 2

c.-7+11T>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2848C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2

Benign 39

c.149+183A>G Multiple submitters
c.150-138T>C Multiple submitters
c.309+291C>G Multiple submitters
c.309+45C>T Multiple submitters
c.310-123C>T Multiple submitters
c.310-212C>A Multiple submitters
c.310-322A>G Multiple submitters
c.*1267G>T Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*133A>T Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*1677T>G Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*1752T>C Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*1788C>T Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*2075C>T Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*2454C>A Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*2658C>T Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*2675C>G Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*3100C>G Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*693G>C Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.*73A>G Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.150-296del Single submitter
c.310-102del Single submitter
c.310-104_310-102del Single submitter
c.310-121_310-119dup Single submitter
c.310-121dup Single submitter
c.-6-301G>T Single submitter
c.-6-324_-6-323del Single submitter
c.*1010G>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1042C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1043G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1124G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1346G>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1525C>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1724C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1908G>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1924T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2163A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2336A>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*3318T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*498A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2

Likely benign 11

c.149+258C>A Multiple submitters
c.310-11G>C Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
c.310-59G>C Multiple submitters
c.310-103_310-102del Single submitter
c.310-14T>A Single submitter
c.*1407C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2761T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*354C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*557G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*569G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
p.Gly23= No assertion criteria MCFD2-related disorder

Uncertain significance 100

p.Ala139Val Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2
p.Ile121Met Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2 ⚠
p.Met79Thr Multiple submitters factor 5 and Factor VIII, combined deficiency of, 2 ⚠
c.-34C>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.-6-8022C>T Single submitter
c.*1024C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1059C>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1079C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1111G>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1151G>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1158C>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1187C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1314C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1316G>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1354G>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1415C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1448G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1464A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1537G>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1610A>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*173G>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1867C>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1875T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*1995G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2017C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2056T>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2106T>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2121G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2128C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2141G>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2169G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*217T>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2423A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2436G>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2556C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2565A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2647A>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2760G>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2789G>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2843T>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*2983T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*3014G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*3099G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*311G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*3272A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*3293A>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*3354A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*3591C>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*375T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*418C>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*422T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*428G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*445A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*517C>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*529G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*62T>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*632T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*640C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*648C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*64T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*751G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*79A>G Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*84T>C Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*892G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*912C>T Single submitter factor 5 and Factor VIII, combined deficiency of, 2
c.*991G>A Single submitter factor 5 and Factor VIII, combined deficiency of, 2
p.Ala139Thr Single submitter ⚠
p.Ala65Val Single submitter ⚠
p.Ala96Val Single submitter ⚠
p.Asn132Ser Single submitter ⚠
p.Asn44Ser Single submitter ⚠
p.Asn85Lys Single submitter ⚠
p.Asp48Asn Single submitter ⚠
p.Cys13Arg Single submitter
p.Gln146Lys Single submitter
p.Gln73Glu Single submitter ⚠
p.Glu107= Single submitter factor 5 and Factor VIII, combined deficiency of, 2
p.Glu114Asp Single submitter ⚠
p.Glu140Lys Single submitter ⚠
p.Glu28Asp Single submitter ⚠
p.Glu66Gln Single submitter ⚠
p.Gly123Cys Single submitter
p.Gly14Ser Single submitter ⚠
p.Gly23Ser Single submitter ⚠
p.Gly37Ser Single submitter ⚠
p.Gly40Ser Single submitter ⚠
p.Gly90Ser Single submitter ⚠
p.His101Tyr Single submitter ⚠
p.Ile118Thr Single submitter
p.Ile120Val Single submitter ⚠
p.Leu117Arg Single submitter ⚠
p.Met3Val Single submitter ⚠
p.Pro36= Single submitter factor 5 and Factor VIII, combined deficiency of, 2
p.Pro36Ala Single submitter factor 5 and Factor VIII, combined deficiency of, 2 ⚠
p.Pro36Ser Single submitter ⚠
p.Pro63Ser Single submitter ⚠
p.Ser32Asn Single submitter ⚠
p.Ser5Cys Single submitter ⚠
p.Val100Ile Single submitter ⚠
p.Val46= Single submitter factor 5 and Factor VIII, combined deficiency of, 2