The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_000488.4(SERPINC1):c.1274G>C (p.Arg425Pro)

CA210752

18009 (ClinVar)

Gene: SERPINC1
Condition: antithrombin III deficiency
Inheritance Mode: Autosomal dominant inheritance
UUID: 448c7154-1578-4ece-aaf2-68c695367358

HGVS expressions

NM_000488.4:c.1274G>C
NM_000488.4(SERPINC1):c.1274G>C (p.Arg425Pro)
NC_000001.11:g.173904010C>G
CM000663.2:g.173904010C>G
NC_000001.10:g.173873148C>G
CM000663.1:g.173873148C>G
NC_000001.9:g.172139771C>G
NG_012462.1:g.18369G>C
ENST00000367698.4:c.1274G>C
ENST00000367698.3:c.1274G>C
ENST00000617423.4:c.659G>C
NM_000488.3:c.1274G>C
NM_001365052.1:c.1130G>C
NM_001365052.2:c.1130G>C
NM_001386302.1:c.1397G>C
NM_001386303.1:c.1355G>C
NM_001386304.1:c.1253G>C
NM_001386305.1:c.1217G>C
NM_001386306.1:c.1058G>C

Likely Pathogenic

Met criteria codes 5
PP3 PS4_Supporting PM5 PM2_Supporting PP1_Moderate

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.1274G>C variant in SERPINC1 is a missense variant predicted to cause substitution of arginine by proline at amino acid 425 (p.Arg425Pro). This variant has been reported in one proband meeting an antithrombin activity level of < 0.8 IU/mL with a family history of antithrombin activity levels of < 0.8 IU/mL (PS4_Supporting; PMID:3828226, 2722864). The variant has been reported to segregate with hereditary antithrombin deficiency in seven affected meioses from the proband's family (PP1_Moderate; PMID: 3828226). The computational predictor REVEL gives a score of 0.878, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3). Another missense variant c.1274G>A (p.Arg425His) (ClinVarID:18019) in the same codon has been classified as pathogenic for hereditary antithrombin deficiency by the ClinGen Thrombosis VCEP (PM5). This variant is absent from gnomAD v2.1.1 and v3.1.2 (PM2_Supporting). 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 VCEP: PM2_Supporting, PS4_Supporting, PP3, PM5, PP1_Moderate.
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.878, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3).
PS4_Supporting
This variant has been reported in one proband meeting an antithrombin activity level of < 0.8 IU/mL with a family history of antithrombin activity levels of < 0.8 IU/mL (PS4_Supporting; PMID:3828226, 2722864).
PM5
Another missense variant c.1274G>A (p.Arg425His) (ClinVarID:18019) in the same codon has been classified as pathogenic for hereditary antithrombin deficiency by the ClinGen Thrombosis VCEP (PM5).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 and v3.1.2 (PM2_Supporting).
PP1_Moderate
The variant has been reported to segregate with hereditary antithrombin deficiency in seven additional affected meioses from one family (PP1_Moderate; PMID: 3828226).
Approved on: 2024-07-03
Published on: 2024-07-03
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.