chr1-173903978-C-T

Position:

• chr1-173903978-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PS4_Moderate PP1_Moderate PP3 PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The c.1306G>A (NM_000488.4) variant in SERPINC1 is a missense variant predicted to cause substitution of alanine by threonine at amino acid 436 (p.Ala436Thr). This variant has been reported in 2 probands meeting an antithrombin activity level of < 0.8 IU/mL with either a family history of antithrombin activity levels of < 0.8 IU/mL or an abnormal crossed immunoelectrophoresis assay demonstrating decreased antithrombin function. One more proband is reported with antithrombin activity levels of < 0.8 IU/mL but no repeat testing or family history is specified so 0.5 point is awarded (PS4_Moderate; PMID:3055413, 1469094). The variant has been reported to segregate with autosomal dominant antithrombin deficiency in 11 affected meioses from one family (PP1_Moderate; PMIDs:1469094, 3055413). The computational predictor REVEL gives a score of 0.778, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3). This variant is absent from gnomAD v2.1.1 and gnomAD v4.1 (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: PP1_Moderate, PM2_Supporting, PS4_Moderate, PP3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA210746/MONDO:0013144/084

• Frequency: Genomes: not found (cov: 32)
• Consequence: SERPINC1 NM_000488.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 7.22

Genes affected

SERPINC1 (HGNC:775): (serpin family C member 1) The protein encoded by this gene, antithrombin III, is a plasma protease inhibitor and a member of the serpin superfamily. This protein inhibits thrombin as well as other activated serine proteases of the coagulation system, and it regulates the blood coagulation cascade. The protein includes two functional domains: the heparin binding-domain at the N-terminus of the mature protein, and the reactive site domain at the C-terminus. The inhibitory activity is enhanced by the presence of heparin. Numerous mutations have been identified for this gene, many of which are known to cause antithrombin-III deficiency which constitutes a strong risk factor for thrombosis. A reduction in the serum level of this protein is associated with severe cases of Coronavirus Disease 19 (COVID-19). [provided by RefSeq, Sep 2020]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINC1	NM_000488.4	c.1306G>A	p.Ala436Thr	missense_variant	7/7	ENST00000367698.4	NP_000479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINC1	ENST00000367698.4	c.1306G>A	p.Ala436Thr	missense_variant	7/7	1	NM_000488.4	ENSP00000356671	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary antithrombin deficiency Pathogenic:3

Likely pathogenic, reviewed by expert panel	curation	Clingen Thrombosis Variant Curation Expert Panel, ClinGen	Aug 16, 2024	The c.1306G>A (NM_000488.4) variant in SERPINC1 is a missense variant predicted to cause substitution of alanine by threonine at amino acid 436 (p.Ala436Thr). This variant has been reported in 2 probands meeting an antithrombin activity level of < 0.8 IU/mL with either a family history of antithrombin activity levels of < 0.8 IU/mL or an abnormal crossed immunoelectrophoresis assay demonstrating decreased antithrombin function. One more proband is reported with antithrombin activity levels of < 0.8 IU/mL but no repeat testing or family history is specified so 0.5 point is awarded (PS4_Moderate; PMID:3055413, 1469094). The variant has been reported to segregate with autosomal dominant antithrombin deficiency in 11 affected meioses from one family (PP1_Moderate; PMIDs:1469094, 3055413). The computational predictor REVEL gives a score of 0.778, which is above the threshold of 0.6, evidence that correlates with impact to SERPINC1 function (PP3). This variant is absent from gnomAD v2.1.1 and gnomAD v4.1 (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: PP1_Moderate, PM2_Supporting, PS4_Moderate, PP3. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 16, 1988	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 29, 2018	For these reasons, this variant has been classified as Pathogenic. Experimental studies using both patient cells and transfected cell lines have shown that cells carrying this missense variant demonstrate reduced antithrombin activity and antigen levels (PMID: 1469094, 16620552). This variant has been reported to segregate with antithrombin deficiency in several families (PMID: 1469094, 16620552). ClinVar contains an entry for this variant (Variation ID: 18003). This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with threonine at codon 436 of the SERPINC1 protein (p.Ala436Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.35
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.91	.;D
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.87
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.90	D;D
M_CAP	Uncertain	0.23	D
MetaRNN	Pathogenic	0.93	D;D
MetaSVM	Uncertain	0.52	D
MutationAssessor	Pathogenic	3.7	.;H
MutationTaster	Benign	1.0	A
PrimateAI	Uncertain	0.60	T
PROVEAN	Uncertain	-2.7	.;D
REVEL	Pathogenic	0.78
Sift	Uncertain	0.0040	.;D
Sift4G	Uncertain	0.0080	D;D
Polyphen		1.0	.;D
Vest4		0.94
MutPred		0.77		.;Gain of phosphorylation at A436 (P = 0.0739);
MVP		0.95
MPC		1.1
ClinPred		1.0	D
GERP RS		5.7
Varity_R		0.93
gMVP		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121909546; hg19: chr1-173873116;