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Variant: NM_000020.3(ACVRL1):c.998G>T (p.Ser333Ile)

CA322708

212802 (ClinVar)

Gene: ACVRL1
Condition: telangiectasia, hereditary hemorrhagic, type 2
Inheritance Mode: Autosomal dominant inheritance
UUID: 9132587e-213d-4925-820b-61a747df77ac
Approved on: 2024-03-15
Published on: 2024-03-15

HGVS expressions

NM_000020.3:c.998G>T
NM_000020.3(ACVRL1):c.998G>T (p.Ser333Ile)
NC_000012.12:g.51915450G>T
CM000674.2:g.51915450G>T
NC_000012.11:g.52309234G>T
CM000674.1:g.52309234G>T
NC_000012.10:g.50595501G>T
NG_009549.1:g.13033G>T
ENST00000547400.6:c.728G>T
ENST00000551576.6:c.998G>T
ENST00000552678.2:c.998G>T
ENST00000388922.9:c.998G>T
ENST00000388922.8:c.998G>T
ENST00000419526.6:c.476G>T
ENST00000550683.5:c.1040G>T
ENST00000552678.1:c.3G>T
NM_000020.2:c.998G>T
NM_001077401.1:c.998G>T
NM_001077401.2:c.998G>T

Pathogenic

Met criteria codes 7
PS4 PS3_Supporting PP3 PP1_Strong PM1 PP4_Moderate PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hereditary Hemorrhagic Telangiectasia Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ACVRL1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Hemorrhagic Telangiectasia VCEP
The NM_000020.3: c.998G>T variant in ACVRL1 is a missense variant predicted to cause substitution of serine by isoleucine at amino acid 333 (p.Ser333Ile). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant has been reported in >4 probands with a phenotype consistent of HHT (PS4; Internal lab contributors). At least one patient's phenotype meets Curacao Criteria for HHT, and sequencing and large deletion/duplication analysis was performed for ENG and ACVRL1, which is highly specific for HHT (PP4_Moderate; Internal lab contributors). The variant has been reported to segregate with disease in a large HHT family (PP1_Strong; Internal lab contributors). This variant resides within a region, Arg329-Asn335 (catalytic loop), of ACVRL1 that is defined as a critical functional domain/residue by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel (PM1). The computational predictor REVEL gives a score of 0.975, which is above the threshold of ≥0.644, evidence that correlates with impact to ACVRL1 function (PP3). Additionally, western blot in HEK293T, COS7 and Hep3B mutant cells showed reduced surface expression of the variant protein and dominant-negative effect. Moreover, the variant induces embryonic dorsalization indicating that this variant impacts protein function (PS3_Supporting; PMID: 16282348). In summary, this variant meets the criteria to be classified as pathogenic for Hereditary Hemorrhagic Telangiectasia based on the ACMG/AMP criteria applied, as specified by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel: PM1, PM2_Supporting, PS4, PS3_Supporting, PP1_Strong, PP3, PP4_Moderate (specification version 1.0.0; 1/04/2024).
Met criteria codes
PS4
This variant has been reported in >4 probands with a phenotype consistent of HHT (PS4; Internal lab contributors).
PS3_Supporting
Western blot in HEK293T, COS7 and Hep3B mutant cells showed reduced surface expression of the variant protein and dominant-negative effect. Moreover, the variant induces embryonic dorsalization indicating that this variant impacts protein function (PS3_Supporting; PMID: 16282348).
PP3
The computational predictor REVEL gives a score of 0.975, which is above the threshold of ≥0.644, evidence that correlates with impact to ACVRL1 function (PP3).
PP1_Strong
The variant has been reported to segregate with disease in a large HHT family (PP1_Strong; Internal lab contributors).
PM1
This variant resides within a region, Arg329-Asn335 (catalytic loop), of ACVRL1 that is defined as a critical functional domain/residue by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel (PM1).
PP4_Moderate
At least one patient's phenotype meets Curacao Criteria for HHT, and sequencing and large deletion/duplication analysis was performed for ENG and ACVRL1, which is highly specific for HHT (PP4_Moderate; Internal lab contributors).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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