NM_000488.4(SERPINC1):c.1235G>A (p.Ser412Asn) AND Hereditary antithrombin deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 14, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002584686.2

Allele description [Variation Report for NM_000488.4(SERPINC1):c.1235G>A (p.Ser412Asn)]

NM_000488.4(SERPINC1):c.1235G>A (p.Ser412Asn)

Gene:

SERPINC1:serpin family C member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q25.1

Genomic location:

Preferred name:

NM_000488.4(SERPINC1):c.1235G>A (p.Ser412Asn)

HGVS:

NC_000001.11:g.173904049C>T
NG_012462.1:g.18330G>A
NM_000488.4:c.1235G>AMANE SELECT
NM_001365052.2:c.1091G>A
NM_001386302.1:c.1358G>A
NM_001386303.1:c.1316G>A
NM_001386304.1:c.1214G>A
NM_001386305.1:c.1178G>A
NM_001386306.1:c.1019G>A
NP_000479.1:p.Ser412Asn
NP_000479.1:p.Ser412Asn
NP_001351981.1:p.Ser364Asn
NP_001373231.1:p.Ser453Asn
NP_001373232.1:p.Ser439Asn
NP_001373233.1:p.Ser405Asn
NP_001373234.1:p.Ser393Asn
NP_001373235.1:p.Ser340Asn
LRG_577t1:c.1235G>A
LRG_577:g.18330G>A
LRG_577p1:p.Ser412Asn
NC_000001.10:g.173873187C>T
NM_000488.3:c.1235G>A

Protein change:

S340N

Molecular consequence:

NM_000488.4:c.1235G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001365052.2:c.1091G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386302.1:c.1358G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386303.1:c.1316G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386304.1:c.1214G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386305.1:c.1178G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386306.1:c.1019G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary antithrombin deficiency
Synonyms:: Antithrombin III deficiency; Thrombophilia due to antithrombin III deficiency; Reduced antithrombin III activity; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013144; MedGen: C0272375; OMIM: 613118; Human Phenotype Ontology: HP:0001976

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003489947	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 14, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003489947

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 14, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003489947.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with SERPINC1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 412 of the SERPINC1 protein (p.Ser412Asn).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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