3-93879306-A-G

Position:

• chr3-93879306-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_000313.4(PROS1):​c.1501T>C​(p.Ser501Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,613,946 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0024 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0032 (8 hom.)
• Consequence: PROS1 NM_000313.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3 U:10 B:1
• Conservation: PhyloP100: -0.0830

Genes affected

PROS1 (HGNC:9456): (protein S) This gene encodes a vitamin K-dependent plasma protein that functions as a cofactor for the anticoagulant protease, activated protein C (APC) to inhibit blood coagulation. It is found in plasma in both a free, functionally active form and also in an inactive form complexed with C4b-binding protein. Mutations in this gene result in autosomal dominant hereditary thrombophilia. An inactive pseudogene of this locus is located at an adjacent region on chromosome 3. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar processing to generate mature protein. [provided by RefSeq, Oct 2015]

PROS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.009359419).
• BS2: High Homozygotes in GnomAdExome4 at 8 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PROS1	NM_000313.4	c.1501T>C	p.Ser501Pro	missense_variant	13/15	ENST00000394236.9	NP_000304.2
PROS1	NM_001314077.2	c.1597T>C	p.Ser533Pro	missense_variant	14/16		NP_001301006.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PROS1	ENST00000394236.9	c.1501T>C	p.Ser501Pro	missense_variant	13/15	1	NM_000313.4	ENSP00000377783.3

Frequencies

GnomAD3 genomes AF: 0.00242 AC: 369 AN: 152186 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000459

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.00137

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00216

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00397

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.00202 AC: 509 AN: 251434 Hom.: 1 AF XY: 0.00218 AC XY: 296 AN XY: 135886

Gnomad AFR exome AF: 0.000431

Gnomad AMR exome AF: 0.00147

Gnomad ASJ exome AF: 0.000198

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00114

Gnomad FIN exome AF: 0.00134

Gnomad NFE exome AF: 0.00332

Gnomad OTH exome AF: 0.00114

GnomAD4 exome AF: 0.00317 AC: 4631 AN: 1461642 Hom.: 8 Cov.: 31 AF XY: 0.00313 AC XY: 2274 AN XY: 727128

Gnomad4 AFR exome AF: 0.000538

Gnomad4 AMR exome AF: 0.00179

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00102

Gnomad4 FIN exome AF: 0.00122

Gnomad4 NFE exome AF: 0.00378

Gnomad4 OTH exome AF: 0.00277

GnomAD4 genome AF: 0.00242 AC: 369 AN: 152304 Hom.: 0 Cov.: 32 AF XY: 0.00230 AC XY: 171 AN XY: 74484

Gnomad4 AFR AF: 0.000457

Gnomad4 AMR AF: 0.00137

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.00216

Gnomad4 NFE AF: 0.00397

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00263 Hom.: 0

Bravo AF: 0.00254

TwinsUK AF: 0.00458 AC: 17

ALSPAC AF: 0.00441 AC: 17

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.00279 AC: 24

ExAC AF: 0.00198 AC: 240

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00284

EpiControl AF: 0.00314

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3 Uncertain:10 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Thrombophilia due to protein S deficiency, autosomal dominant Pathogenic:1 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	Nov 21, 2018	- -
Uncertain significance, no assertion criteria provided	clinical testing	Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	Oct 09, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Feb 16, 2018	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Likely pathogenic, criteria provided, single submitter	clinical testing	ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology	-	- -

not provided Pathogenic:1 Uncertain:2

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Sep 18, 2024	PP5, PS3, PS4 -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The PROS1 p.Ser533Pro variant, also commonly referred to as the Heerlen variant, was identified in 141 of 11096 proband chromosomes (frequency: 0.0127) from individuals or families with venous thrombosis or Protein S deficiency (Labrouche_2003_PMID:12960605, Bertina_1990_PMID:2143091, Suchon_2017_PMID:28374852, Borgel_1996_PMID:8765219).The variant was identified in dbSNP (ID: rs121918472) and ClinVar (classified as a VUS by Invitae and Equipe Genetique des Anomalies du Developpement, Université de Bourgogne in 2018 and as likely benign by PreventionGenetics). The variant was identified in control databases in 570 of 282838 chromosomes (1 homozygous) at a frequency of 0.002015 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 425 of 129150 chromosomes (freq: 0.003291), European (Finnish) in 37 of 25124 chromosomes (freq: 0.001473), Latino in 51 of 35432 chromosomes (freq: 0.001439), Other in 10 of 7226 chromosomes (freq: 0.001384), South Asian in 35 of 30616 chromosomes (freq: 0.001143), African in 9 of 24970 chromosomes (freq: 0.00036), Ashkenazi Jewish in 2 of 10368 chromosomes (freq: 0.000193), and East Asian in 1 of 19952 chromosomes (freq: 0.00005). Evidence for this variant’s role in protein S (encoded by PROS1) deficiency and venous thrombosis is conflicting. One study identified that the variant segregated with protein S deficiency in seven families, though a few carriers were unaffected (Duchemin_1995_PMID:7579448). Other studies have also found that the variant segregates with protein S deficiency, and that individuals homozygous for the Heerlen variant have been reported to have lower protein S levels and a more severe type I form compared to individuals that are heterozygous (Espinosa-Parilla_2000_PMID:10669162). Several studies report a statistically significant increase in the Heerlen allele frequency in individuals with low protein S levels and/or venous thrombosis (Borgel_1996_PMID:8765219, Duchemin_1995_PMID:7579448, Suchon_2017_PMID:28374852). However, other studies have identified the variant at a similar frequency in controls as well as affected individuals (PMID: Bertina_1990_2143091, Pintao_2013_PMID:24014240). One functional study reports a synergy with Factor V Leiden mutation and a reduced capacity for the Heerlen variant to act as a co-factor for APC (Giri_2010_PMID:10887114). Therefore it is unclear at this time if the Heerlen variant is pathogenic for venous thrombosis or Protein S deficiency, however it may contribute risk in conjuction with other genetic factors. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Ser533 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 15, 2020	Identified in multiple heterozygous individuals with protein S deficiency and some of these individuals have a history of thrombosis (Duchemin et al., 1995; Borgel et al., 1996; Espinosa-Parrilla et al., 2000; Labrouche et al., 2003; Beauchamp et al., 2004; ten Kate et al., 2008; Suchon et al., 2017; Wypasek et al., 2017); Reported in at least one asymptomatic homozygous individual with type I protein S deficiency and protein S levels lower than heterozygous individuals (Espinosa-Parilla et al., 2000; Giri et al., 2000); Segregates with protein S deficiency in multiple relatives from unrelated families; however, it was absent from some relatives with protein S deficiency, and it has been found in relatives without protein S deficiency, as well as in unrelated control individuals (Duchemin et al., 1995; Espinosa-Parrilla et al., 1997; Beauchamp et al., 2004; ten Kate et al., 2008); Several individuals with a history of thrombotic events who harbored this variant also harbored additional variants, including factor V Leiden (Borgel et al., 1996; Espinosa-Parrilla et al., 2000; Wypasek et al., 2014; Bruwer et al., 2016); Although at least one early study found no significant difference in the frequency of this variant in individuals with thrombophilia versus controls, a subsequent larger study did find an increased frequency of this variant in individuals with venous thrombosis, with an estimated odds ratio of 6.57 (Bertina et al., 1990; Suchon et al., 2017); Published in vitro assays demonstrate that the S501P variant is associated with faster clearance than wild-type protein S (Denis et al., 2005); An additional functional study suggests that S501P displays deficient APC-cofactor activity in the degradation of factor V Leiden and that there may be synergistic effects between thrombophilic risk factors, while another study reports that S501P has no impact on APC-cofactor and APC-independent coagulation activities (Giri et al., 2000; Koenen et al., 2004); In silico analysis supports that this missense variant does not alter protein structure/function; Also described as the Heerlen allele/polymorphism or S460P using alternate nomenclature; This variant is associated with the following publications: (PMID: 9108398, 15175796, 10887114, 18841302, 24119292, 29883906, 27838551, 18435454, 24365770, 24014240, 12960605, 8765219, 20880255, 31019283, 7579448, 10669162, 28607330, 28374852, 2143091, 15147381, 16100035, 21764424, 22273984) -

not specified Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 04, 2019	The p.Ser501Pro variant in PROS1 (also reported as p.Ser460Pro or PS Heerlen) has been identified in >20 individuals with protein S deficiency type III (Duchemin 1995, Espinosa-Parrilla 2000, Beachamp 2004, ten Kate 2008, Varvenne 2011, Mulder 2012, Wypasek 2014). While the variant segregated with protein S deficiency in >10 affected family members (Duchemin 1995, Espinosa-Parrilla 2000, Beachamp 2004, ten Kate 2008), there were also multiple individuals in these families who had protein S deficiency but were negative for the p.Ser501Pro variant (Espinosa-Parrilla 2000, ten Kate 2008). Computational prediction tools and conservation analysis suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In vivo and in vitro functional studies provide some evidence that this variant may impact protein S function (Duchemin 1995, Denis 2005); however, these types of assays may not accurately represent biological function. This variant has also been identified in individuals with normal protein S levels (Espinosa-Parrilla 2000, Beauchamp 2004, ten Kate 2008) and in 0.33% (425/129150) of European chromosomes in gnomAD (http://gnomad.broadinstitute.org). The variant is also present in ClinVar with conflicting interpretations (Variation ID: 13316). While one meta-analysis has reported an odds ratio of 4-10 for venous thrombosis in French individuals who are heterozygous for this variant (Suchon 2017), this result has not been replicated. Furthermore, other studies find no association between this or other PROS1 variants and the risk for thrombosis (Alhenc-Gelas 2010, Pintao 2013). In summary, given the conflicting data regarding the impact of this variant on plasma protein S levels and risk for thrombosis, the clinical significance of the p.Ser501Pro variant is uncertain. ACMG/AMP criteria applied: PP1_Strong, PS3_Supporting, BS4, BS1_Supporting, BP4. -
Likely benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Protein S Heerlen Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 01, 2004

- -

Optic atrophy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg

Jan 01, 2023

- -

Hereditary thrombophilia due to congenital protein S deficiency Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genetics and Molecular Pathology, SA Pathology

Sep 15, 2021

- -

Thrombophilia due to protein S deficiency, autosomal recessive Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 27, 2022

This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 501 of the PROS1 protein (p.Ser501Pro). This variant is present in population databases (rs121918472, gnomAD 0.3%), including at least one homozygous and/or hemizygous individual. This variant is known as the Heerlen variant, also reported as Ser460Pro. This variant has been reported in several individuals with type III protein S deficiency and it segregates with disease in multiple families but some carriers are unaffected (PMID: 7579448, 1547381, 12960605, 24119292). The pathogenicity of this variant is much debated in the literature with reports that argue for a pathogenic classification, a benign polymorphism as well as a modifier that works in synergy with other genetic factors. It has also been observed to segregate with disease in related individuals. This variant has been classified as a polymorphism in some reports because it is present at a similar frequency in controls as well as affected individuals (PMID: 2143091, 24014240) and it has been reported in unaffected family members (PMID: 15147381). In contrast, several studies report a statistically significant increase in the Heerlen allele frequency in individuals with low protein S levels and/or venous thrombosis (PMID: 8765219, 7579448, 10669162, 28374852). In addition, individuals homozygous for Heerlen have been reported to have lower protein S levels and a more severe type I form compared to individuals that are heterozygous (PMID: 10887114, 10669162). Finally, several reports suggest that the Heerlen variant shows synergy with other genetic risks for thrombosis such as Factor V Leiden and/or APC (activated protein C) variants (PMID: 8765219, 10669162, 20880255, 24365770). One functional study reports a synergy with Factor V Leiden mutation and a reduced capacity for the Heerlen variant to act as a co-factor for APC (PMID: 10887114). ClinVar contains an entry for this variant (Variation ID: 13316). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PROS1 protein function. In conclusion, there is evidence to support increased risk for protein S deficiency in heterozygous individuals and homozygous individuals show a more severe deficiency, although this variant has also been reported in unaffected family members and in control individuals. There is also evidence to support that the Heerlen variant alone has a mild effect but acts in synergy with other genetic factors. Because there is support for both a pro-pathogenic and a pro-benign effect, this sequence change has been classified as Uncertain Significance. -

Retinal dystrophy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg

Jan 01, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	6.5
DANN	Benign	0.83
DEOGEN2	Uncertain	0.46	T;.;.;T;.;.
Eigen	Benign	-0.92
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.066	N
LIST_S2	Benign	0.74	.;T;T;T;T;T
M_CAP	Benign	0.048	D
MetaRNN	Benign	0.0094	T;T;T;T;T;T
MetaSVM	Benign	-0.31	T
MutationAssessor	Benign	1.4	L;.;.;L;.;.
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.0	N;.;.;.;.;.
REVEL	Uncertain	0.37
Sift	Benign	0.13	T;.;.;.;.;.
Sift4G	Benign	0.099	T;.;.;.;.;.
Polyphen		0.84	P;.;.;P;.;.
Vest4		0.35
MVP		0.79
MPC		0.29
ClinPred		0.0041	T
GERP RS		-3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.11
gMVP		0.58

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: rs121918472; hg19: chr3-93598150;