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Variant: NM_000138.5(FBN1):c.5443G>A (p.Gly1815Ser)

CA015829

200064 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: b5cf8ff9-2cd0-4a4b-9b07-2557d4dfb631
Approved on: 2022-12-01
Published on: 2022-12-01

HGVS expressions

NM_000138.5:c.5443G>A
NM_000138.5(FBN1):c.5443G>A (p.Gly1815Ser)
NC_000015.10:g.48452664C>T
CM000677.2:g.48452664C>T
NC_000015.9:g.48744861C>T
CM000677.1:g.48744861C>T
NC_000015.8:g.46532153C>T
NG_008805.2:g.198125G>A
ENST00000684448.1:n.4117G>A
ENST00000316623.10:c.5443G>A
ENST00000674301.1:n.442G>A
ENST00000316623.9:c.5443G>A
ENST00000537463.6:c.*1206G>A
ENST00000559133.5:n.750G>A
NM_000138.4:c.5443G>A
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Uncertain Significance

Met criteria codes 1
BP2
Not Met criteria codes 25
PVS1 PS2 PS4 PS3 PS1 BA1 PP4 PP1 PP3 PP2 PM4 PM3 PM1 PM5 PM6 PM2 BS4 BS3 BS1 BS2 BP7 BP5 BP3 BP4 BP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_00138 c.5443G>A is a missense variant in FBN1 predicted to cause a substitution of a Glycine by Serine at amino acid 1815 (p.Gly1815Ser). This variant has been reported 3 times in ClinVar: once as likely pathogenic and twice as a variant of uncertain significance (Variation ID: 200064). This variant has been reported in the literature in 2 probands. It was identified in the homozygous state in an individual with autism spectrum disorder, global developmental delays, arachnodactyly, and dysmorphic features (PMID: 32655337); of note, homozygous variants of uncertain significance were identified in two other genes in this individual, and all 3 homozygous variants were found to segregate with disease in a similarly affected sibling. It was identified in another individual with sudden unexplained death in epilepsy, for which an autopsy did not identify any cardiac abnormalities (PMID: 27930701). This variant was also identified in an internal proband with thoracic aortic dissection and a systemic score >7 however, a pathogenic nonsense variant in FBN1 was also identified in this individual (BP2) and was considered to explain the phenotype . This variant has been identified in 0.0033% of individuals of South Asian origin in gnomAD v2.1.1. (https://gnomad.broadinstitute.org/). Computational prediction tools and conservation analysis are unclear on the predicted impact on the protein. The constraint z-score for missense variants affecting FBN1 is 5.06 however due to the presence of one benign argument PP2 cannot be used . In summary, this variant meets the criteria to be classified as uncertain significance for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: BP2
Met criteria codes
BP2
Another nonsense variant in FBN1 has been found
Not Met criteria codes
PVS1
N/A for this variant
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
neither proband in literature has phenotype consistent enough with MFS to count as probands
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
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Patient meets revised Ghent criteria (TAD, systemic score >7), however another pathogenic variant was also identified in this individual
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL: 0.596
PP2
Although constrain score for missense variants is 5.06, PP2 should not be used given the application of benign arguments
PM4
N/A for this variant
PM3
N/A for FBN1
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
MAF: 0.003266% greater than 0.0005% cutoff per VCEP (gnomAD v2.1.1)
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
N/A for this variant
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
N/A for this gene
BP4
REVEL: 0.596 which above the threshold of 0.326
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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