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Variant: NM_000138.5(FBN1):c.3058A>G (p.Thr1020Ala)

CA013721

42325 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: a9eca109-fab3-4831-8e73-603490ebe5b6

HGVS expressions

NM_000138.5:c.3058A>G
NM_000138.5(FBN1):c.3058A>G (p.Thr1020Ala)
NC_000015.10:g.48489875T>C
CM000677.2:g.48489875T>C
NC_000015.9:g.48782072T>C
CM000677.1:g.48782072T>C
NC_000015.8:g.46569364T>C
NG_008805.2:g.160914A>G
ENST00000684448.1:n.1732A>G
ENST00000316623.10:c.3058A>G
ENST00000316623.9:c.3058A>G
ENST00000537463.6:c.637-15225A>G
NM_000138.4:c.3058A>G

Likely Benign

Met criteria codes 3
BS1 BP5 BP2
Not Met criteria codes 19
BA1 BS4 BS3 BS2 BP4 BP1 PS2 PS4 PS3 PS1 PP3 PP2 PP4 PP1 PM3 PM1 PM5 PM6 PM2

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.3058A>G, is a missense variant in FBN1 predicted to cause a substitution of a Threonine by Alanine at amino acid 1020 (p.Thr1020Ala). This variant was found in 12 probands with variable phenotypes, mostly thoracic aortic aneurysm or a marfanoid habitus. One proband additionally presented ectopia lentis. Two of these probands carried two other pathogenic variants: a variant in FBN1 (BP2) and a variant in TGFBR1 (BP5). The variant in FBN1 has been reported ten times in ClinVar: 8 times as likely benign and two times as a variant of uncertain significance (Variation ID: 42325). The variant has been reported in the literature in multiple affected individuals including one individual with classical Marfan syndrome (PMID: 11175294), one individual with incomplete Marfan syndrome (PMID: 18435798), one patient with MASS syndrome (PMID: 25944730), and an individual with bicuspid aortic valve and aortic root aneurysm (PMID: 28387797). This variant has also been reported in 3 patients with Lujan-Fryns syndrome (PMID: 19293843, PMID: 28027854), including two brothers with marfanoid habitus, learning disabilities without cardiac defects (PMID: 28027854). These brothers also share a variant in MECP2. Segregation analysis in one family showed that the variant was also present in four additional family members, none of which had aortic aneurysm, two had a marfanoid habitus This variant has been identified in 80 individuals of European-non-Finnish origin (MAF: 0.062%) in gnomad v2.1.1 (https://gnomad.broadinstitute.org/) (BS1). 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 likely benign for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: BS1, BP2, BP5.
Met criteria codes
BS1
Frequency in NFE of 0.062% (80/129022) which is between 0.005-0.1%
BP5
One proband with another variant in TGFBR1
BP2
One porband had another pathogenic variant in FBN1
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
BS2
Not applicable for MFS
BP4
REVEL score of 0.388 which is just aboven the threshold of 0.326
BP1
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
BS1 criteria applied
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
PP3
REVEL score of 0.388
PP2
Cannot Apply PP2 with other benign arguments
PP4
No to be used because BS1 and BP2 apply
PP1
4 additional family members have the variant. None have aortic aneurysm, 2 have Marfanoid habitus
PM3
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
The variant FBN1 c.3059C>G (p.Thr 1020Arg) is classified as VUS
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2022-12-01
Published on: 2022-12-01
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