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.4466A>G (p.Asn1489Ser)

CA16042872

373598 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 6ca054ea-0c20-4074-a5a8-c5e121fbabfb

HGVS expressions

NM_000138.5:c.4466A>G
NM_000138.5(FBN1):c.4466A>G (p.Asn1489Ser)
NC_000015.10:g.48468528T>C
CM000677.2:g.48468528T>C
NC_000015.9:g.48760725T>C
CM000677.1:g.48760725T>C
NC_000015.8:g.46548017T>C
NG_008805.2:g.182261A>G
ENST00000684448.1:n.3140A>G
ENST00000316623.10:c.4466A>G
ENST00000316623.9:c.4466A>G
ENST00000537463.6:c.*229A>G
NM_000138.4:c.4466A>G

Uncertain Significance

Met criteria codes 3
PM2 PM5 PP2
Not Met criteria codes 23
PM6 PS2 PS4 PS3 PS1 PM4 PM3 PM1 BA1 PVS1 BP7 BP5 BP3 BP2 BP4 BP1 BS2 BS4 BS3 BS1 PP4 PP1 PP3

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.4466A>G variant is a missense variant in FBN1 predicted to cause a substitution of asparagine by serine at amino position 1489. This variant has not been reported in the literature but has been reported in ClinVar three times as a variant of uncertain significance (Variation ID: 373598). This variant lies in a critical calcium binding site within a calcium-binding EGF domain; however, since asparagine to serine substitutions in these positions might be tolerated (PMID: 31227806) the PM1 criterion has not been used. It is not present in gnomAD v2.1.1 nor v3.1.2 (PM2_supporting; https://gnomad.broadinstitute.org/). Computational prediction tools and conservation analysis are unclear about the predicted impact of this variant (REVEL = 0.556). The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). Another missense variant at the same position (p.Asn1489Lys) is classified as likely pathogenic (PM5; PMIDs: 20082464, 26621581; 21542060). Due to the insufficient evidence, this variant is classified as of uncertain significance for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PM2_supporting, PP2, PM5.
Met criteria codes
PM2
absent from gnomAD v2.1.1 and v3.1.2
PM5
p.Asn1489Lys is Likely Pathogenic per FBN1 VCEP specifications: PS4_moderate, PM1, PM2_supporting, PP1
PP2
missense variant, no benign criteria asserted
Not Met criteria codes
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
<1.0 PS4 points
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
no evidence
PM4
n/a
PM3
n/a for FBN1
PM1
consensus calcium-binding sequence in cbEGF22; Asparagine>Serine may be tolerated at this position
BA1
PM2_supporting met
PVS1
n/a
BP7
n/a
BP5
no evidence
BP3
n/a for FBN1
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL = 0.556
BP1
n/a for FBN1
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
not necessarily a non-segregation (Invitae)
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
PM2_supporting met
PP4
no evidence
PP1
only 1 segregation and it is only with the scoliosis component of the proband's phenotype (Invitae)
PP3
REVEL = 0.556
Approved on: 2023-06-15
Published on: 2023-06-15
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