The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000488.4(SERPINC1):c.235C>A (p.Arg79Ser)

CA210760

18015 (ClinVar)

Gene: SERPINC1
Condition: antithrombin III deficiency
Inheritance Mode: Autosomal dominant inheritance
UUID: 218b52f4-b409-42b8-b64c-6427824168a4
Approved on: 2024-05-09
Published on: 2024-05-09

HGVS expressions

NM_000488.4:c.235C>A
NM_000488.4(SERPINC1):c.235C>A (p.Arg79Ser)
NC_000001.11:g.173914726G>T
CM000663.2:g.173914726G>T
NC_000001.10:g.173883864G>T
CM000663.1:g.173883864G>T
NC_000001.9:g.172150487G>T
NG_012462.1:g.7653C>A
ENST00000367698.4:c.235C>A
ENST00000367698.3:c.235C>A
ENST00000494024.1:n.461C>A
ENST00000617423.4:c.235C>A
NM_000488.3:c.235C>A
NM_001365052.1:c.91C>A
NM_001365052.2:c.91C>A
NM_001386302.1:c.235C>A
NM_001386303.1:c.316C>A
NM_001386304.1:c.235C>A
NM_001386305.1:c.235C>A
NM_001386306.1:c.235C>A

Likely Pathogenic

Met criteria codes 5
PP3 PM1 PM5 PM2_Supporting PS4_Supporting
Not Met criteria codes 1
PS3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Thrombosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SERPINC1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Thrombosis VCEP
The c.235C>A variant in SEPRINC1 is a missense variant predicted to cause substitution of arginine by serine at amino acid 79 (p.Arg79Ser). This variant has been reported in one family with an abnormal crossed immunoelectrophoresis assay demonstrating decreased antithrombin function. (PS4_Supporting; PMID:3350974). This variant is absent from gnomAD v[2.1.1] (PM2_Supporting). This variant resides within a region, Arg79, of SERPINC1 that is defined as a critical functional domain that would impact heparin binding site residues by the ClinGen Thrombosis Variant Curation Expert Panel (PM1). Another missense variant c.236G>A (p.Arg79His) (ClinVarID:18014) in the same codon has been classified as pathogenic for hereditary antithrombin deficiency by the ClinGen Thrombosis Variant Curation Expert Panel (PM5). The computational predictor REVEL gives a score of 0.718, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant hereditary antithrombin deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Thrombosis Variant Curation Expert Panel: PM1, PM5, PP3, PM2_Supporting, PS4_Supporting. (Required: ClinGen Thrombosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SERPINC1 Version 1.0.0; date of approval)
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.718, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3).
PM1
This variant resides within a region, Arg79, of SERPINC1 that is defined as a critical functional domain that would impact heparin binding site residues by the ClinGen Thrombosis Variant Curation Expert Panel (PM1).
PM5
Another missense variant c.236G>A (p.Arg79His) (ClinVarID:18014) in the same codon has been classified as pathogenic for hereditary antithrombin deficiency by the ClinGen Thrombosis Variant Curation Expert Panel (PM5).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4_Supporting
This variant has been reported in one family with an abnormal crossed immunoelectrophoresis assay demonstrating decreased antithrombin function. (PS4_Supporting; PMID:3350974).
Not Met criteria codes
PS3
Functional data soon to be published after ISTH 2024. To be added later.
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