The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000488.4(SERPINC1):c.1301T>G (p.Phe434Cys)

CA343772451

627224 (ClinVar)

Gene: SERPINC1
Condition: antithrombin III deficiency
Inheritance Mode: Autosomal dominant inheritance
UUID: d46c80fa-aeac-4d2d-a3eb-c74213ad1557
Approved on: 2024-02-19
Published on: 2024-02-19

HGVS expressions

NM_000488.4:c.1301T>G
NM_000488.4(SERPINC1):c.1301T>G (p.Phe434Cys)
NC_000001.11:g.173903983A>C
CM000663.2:g.173903983A>C
NC_000001.10:g.173873121A>C
CM000663.1:g.173873121A>C
NC_000001.9:g.172139744A>C
NG_012462.1:g.18396T>G
ENST00000367698.4:c.1301T>G
ENST00000367698.3:c.1301T>G
ENST00000617423.4:c.686T>G
NM_000488.3:c.1301T>G
NM_001365052.1:c.1157T>G
NM_001365052.2:c.1157T>G
NM_001386302.1:c.1424T>G
NM_001386303.1:c.1382T>G
NM_001386304.1:c.1280T>G
NM_001386305.1:c.1244T>G
NM_001386306.1:c.1085T>G
More

Uncertain Significance

Met criteria codes 4
PS4_Supporting PM5_Supporting PM2_Supporting PP3

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.1301T>G (NM_000488.4) variant in SERPINC1 is a missense variant predicted to cause substitution of phenylalanine by cystenine at amino acid 434 (p.Phe434Cys). This variant has been reported in 1 proband meeting an antithrombin activity level of < 0.8 IU/mL with repeat testing overtime (PS4_Supporting; PMID:1469094). This variant is absent from gnomAD v3.1.2 and v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.921, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3). Another missense variant c.1302C>A (p.Phe434Leu) (ClinVarID:2202884) in the same codon has been classified as likely pathogenic for autosomal dominant antithrombin III deficiency by the ClinGen Thrombosis VCEP (PM5_Supporting). In summary, this variant meets the criteria to be classified as uncertain significance due to insufficient evidence for autosomal dominant antithrombin III deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Thrombosis VCEP: PP3, PM2, PM5, PS4_Supporting. (ClinGen Thrombosis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SERPINC1 Version 1.0.0; date of approval)
Met criteria codes
PS4_Supporting
This variant has been reported in 1 proband meeting an antithrombin activity level of < 0.8 IU/mL with repeat testing overtime (PS4_Supporting; PMID:1469094).
PM5_Supporting
Another missense variant c.1302C>A (p.Phe434Leu) (ClinVarID:2202884) in the same codon has been classified as likely pathogenic for autosomal dominant antithrombin III deficiency by the ClinGen Thrombosis VCEP (PM5_Supporting).
PM2_Supporting
This variant is absent from gnomAD v2.1.1,v3.1.2 and v4.0.0 (PM2_Supporting).
PP3
The computational predictor REVEL gives a score of 0.921, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3).
Curation History
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.