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Variant: NM_000138.5(FBN1):c.3509G>A (p.Arg1170His)

CA014215

16451 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: bbe2b789-1955-4672-a1a5-d8ee020aa9d6

HGVS expressions

NM_000138.5:c.3509G>A
NM_000138.5(FBN1):c.3509G>A (p.Arg1170His)
NC_000015.10:g.48487155C>T
CM000677.2:g.48487155C>T
NC_000015.9:g.48779352C>T
CM000677.1:g.48779352C>T
NC_000015.8:g.46566644C>T
NG_008805.2:g.163634G>A
ENST00000684448.1:n.2183G>A
ENST00000316623.10:c.3509G>A
ENST00000316623.9:c.3509G>A
ENST00000537463.6:c.637-12505G>A
NM_000138.4:c.3509G>A

Benign

Met criteria codes 3
BP5 BP2 BA1
Not Met criteria codes 13
BP4 BP1 PS4 PS3 PS1 PP1 PP3 PP2 PM2 PM1 PM5 BS3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_00138 c.3509G>A, is a missense variant in FBN1 predicted to cause a substitution of an arginine acid by histidine at amino acid 1170 (p.Arg1170His). This variant has been previously reported in several apparently unrelated individuals with Marfan syndrome (PMID 26787436, internal data), incomplete Marfan syndrome, including with skeletal features and/or mitral valve prolapse (PMID 7870075, 9837823, 17418587, 17627385, 17657824), in individuals with isolated thoracic aortic aneurysm and/or dissection (internal data) and in other phenotypes like arterial dissection and venous bleeding (internal data). This variant was found to segregate with disease in seven affected individuals with incomplete Marfan syndrome from three families (PMID 7870075, 9837823, internal data). This variant has been found to co-occur with different pathogenic variants in FBN1 (BP2), TGFBR1, and TGFRB2 (BP5) (internal data). This variant has been identified in 286 individuals of European non-Finnish origin (MAF: 0.2%) (BA1; https://gnomad.broadinstitute.org/, version 2.1.1). The variant in FBN1 has been reported 21 times in ClinVar: 16 times as likely benign and 5 times as uncertain significance (Variation ID: 16451). Computational prediction tools and conservation analysis are unclear on the predicted impact on the protein (REVEL: 0.502). Functional studies, including in-vitro splicing analysis, found that this variant had no impact on splicing (PMID 21895641, 32123317). The constraint z-score for missense variants affecting FBN1 is 5.06, however due to the presence of benign arguments, PP2 cannot be used. In summary, this variant meets criteria to be classified as benign for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: BA1, BP2, BP5.
Met criteria codes
BP5
Internal data: 1 proband with pathogenic variant in TGFBR11 proband with pathogenic variant in TGFBR2
BP2
Found to co-occur in two probands with different pathogenic variants in FBN1. Phasing not provided  ClinVar LabCorp of American submission:Found to co-occur with two pathogenic variants in FBN1: c.4913delA, p.Tyr1638fs*2 and c.1633C>T, p.Arg545Cys
BA1
European non-Finnish ethnic population 0.2%
Not Met criteria codes
BP4
REVEL: 0.502
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
n/a because BA1 is met Probands with dx with MFS PMID 26787436- Four probands Probands with incomplete MFS (including skeletal features and/or mitral valve prolapse: Each with one proband with incomplete MFS: PMID 7870075 (One proband with dolichostenomelia and arachnodactyly), 9837823, 17418587, 17627385, 17657824) Additional data not included in variant summary: PMID 25852444- identified in one individual with hypotonia and developmental delay, but no dx of MFS. PMID 31211626- Identified in >40 individuals ascertained through a biobank (phenotypes not clear)
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
n/a given application of BA1Identified in seven affected individuals from three families, however phenotypes are skeletal/systemic features, without EL or TAAD:  PMID 7870075- Identified in proband and one affected relative (m=1) PMID 9837823- Identified in proband and two affected relatives (m=2) Internal data (UZG)- Identified in proband and one affected relative (m=1)
PP3
REVEL: 0.502
PP2
n/a- benign criteria met
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
FBN1 p.Arg1170Cys. classified as a VUS, but should not be considered here in any case given that creating a Cys in a cb-EGF domain could have a different effect than creating a His
BS3
Two studies evaluating in-vitro splicing found that this variant had no impact on splicing (PMID 21895641, 32123317)
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-02-01
Published on: 2023-02-01
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