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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

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Published on: January 16, 2019

Genetic variants associated with protein C levels.

C Y Vossen¹, B P Koeleman, S J Hasstedt

¹Department of Medical Genetics, University Medical Center Utrecht, Utrecht, Netherlands.

Journal of Thrombosis and Haemostasis : JTH

|February 8, 2013

Summary

Researchers identified four genes at chromosome 5q14.1 that may influence normal protein C (PC) levels. BHMT2 is a likely candidate for regulating PC levels through homocysteine, impacting thrombin inhibition.

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Published on: July 18, 2017

Area of Science:

Genetics
Molecular Biology
Thrombosis Research

Background:

Normal protein C (PC) plasma levels exhibit wide variation.
Factors influencing PC levels are linked to venous thrombosis risk.
Genetic variants affecting normal PC levels are largely unknown.

Purpose of the Study:

To conduct a genome scan to identify genes regulating normal protein C (PC) levels.
To explore the genetic basis of PC plasma level variability.
To identify genetic variants associated with normal PC levels and thrombosis risk.

Main Methods:

Variance components linkage analysis in a large family (275 individuals).
Next-generation sequencing of candidate genes within a linkage peak.
Re-evaluation of linkage conditional on genotype effects and replication in the Leiden Thrombophilia Study (LETS).

Main Results:

A quantitative trait locus on chromosome 5q14.1 associated with PC level variability was identified.
Four single nucleotide polymorphisms (SNPs) in BHMT2, ACOT12, SSBP2, and XRCC4 were found to increase PC levels in the studied family.
Replication in the LETS cohort was unsuccessful, potentially due to genetic background differences.

Conclusions:

Four genes located at chromosome 5q14.1 may influence normal protein C (PC) levels.
BHMT2 is a strong candidate for regulating PC levels, possibly via homocysteine's interaction with thrombin.
Discrepancies in replication suggest variations in genetic background and linkage disequilibrium between study populations.