The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000138.5(FBN1):c.2669G>A (p.Cys890Tyr)

CA392331935

431935 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 797259f6-a65f-4f86-b079-056f10bb550d
Approved on: 2023-06-15
Published on: 2023-06-15

HGVS expressions

NM_000138.5:c.2669G>A
NM_000138.5(FBN1):c.2669G>A (p.Cys890Tyr)
NC_000015.10:g.48495131C>T
CM000677.2:g.48495131C>T
NC_000015.9:g.48787328C>T
CM000677.1:g.48787328C>T
NC_000015.8:g.46574620C>T
NG_008805.2:g.155658G>A
ENST00000684448.1:n.1343G>A
ENST00000316623.10:c.2669G>A
ENST00000316623.9:c.2669G>A
ENST00000537463.6:c.637-20481G>A
NM_000138.4:c.2669G>A
More

Likely Pathogenic

Met criteria codes 7
PP4 PP3 PP2 PM5 PM1 PM2_Supporting PM6
Not Met criteria codes 19
PS4 PS2 PS3 PS1 BP3 BP2 BP4 BP1 BP7 BP5 BA1 PP1 PVS1 PM4 PM3 BS2 BS4 BS3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen FBN1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_000138 c.2669G>A variant is a missense variant in FBN1 predicted to cause a substitution of cysteine by tyrosine at amino acid position 890. This variant has not been reported in the literature but was identified at one institution as de novo in proband with ectopia lentis and a systemic score of 2 (PP4, PM6; UZG). This variant has also been reported four times in ClinVar, with two classifications of likely pathogenic and two classifications of pathogenic (Variation ID: 431935). It is not present in gnomAD v2.1.1 or 3.1.2 (PM2_supporting; https://gnomad.broadinstitute.org/). This variant affects a cysteine residue in the hybrid 2 domain; cysteine residues in the hybrid domains are believed to be important for proper protein folding (PM1). Computational prediction tools and conservation analysis support that this variant may impact the protein (PP3; REVEL = 0.926). The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). Three other missense variants at the same amino acid position (p.Cys890Arg, p.Cys890Gly, p.Cys890Trp) have been identified and are classified as likely pathogenic (PM5; PMIDs: 12938084, 16222657, 20564469). In summary, this variant meets criteria to be classified as likely pathogenic for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PM1, PM5, PM6, PM2_supporting, PP2, PP3, PP4.
Met criteria codes
PP4
6yo proband with EL + SS =2 (facial features, pectus excavatum), no TAAD; VCEP determined that based on the specificity of ectopia lentis to FBN1 and the proband's young age, PP4 would be applied
PP3
REVEL = 0.926
PP2
missense variant, no benign criteria asserted
PM5
p.Cys890Arg, p.Cys890Gly, and p.Cys890Trp all likely pathogenic per VCEP specifications
PM1
Cys in Hyb2 domain
PM2_Supporting
absent from gnomAD v2.1.1 and v3.1.2
PM6
6yo proband with EL + SS =2 (facial features, pectus excavatum), no TAAD; VCEP determined that based on the specificity of ectopia lentis to FBN1, in addition to some systemic features, and the proband's young age, PM6 would be applied
Not Met criteria codes
PS4
no evidence
PS2
no evidence
PS3
no evidence
PS1
no evidence
BP3
n/a for FBN1
BP2
n/a for FBN1
BP4
PP3 met
BP1
n/a for FBN1
BP7
n/a
BP5
no evidence
BA1
PM2_supporting met
PP1
no evidence
PVS1
n/a
PM4
n/a
PM3
n/a for FBN1
BS2
no evidence
BS4
no evidence
BS3
no evidence
BS1
PM2_supporting met
Curation History
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