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NM_000488.4(SERPINC1):c.670A>T (p.Asn224Tyr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 18, 2019
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:
RCV001027531.2

Allele description [Variation Report for NM_000488.4(SERPINC1):c.670A>T (p.Asn224Tyr)]

NM_000488.4(SERPINC1):c.670A>T (p.Asn224Tyr)

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.670A>T (p.Asn224Tyr)
HGVS:
  • NC_000001.11:g.173910846T>A
  • NG_012462.1:g.11533A>T
  • NM_000488.4:c.670A>TMANE SELECT
  • NM_001365052.2:c.526A>T
  • NM_001386302.1:c.670A>T
  • NM_001386303.1:c.751A>T
  • NM_001386304.1:c.670A>T
  • NM_001386305.1:c.670A>T
  • NM_001386306.1:c.454A>T
  • NP_000479.1:p.Asn224Tyr
  • NP_000479.1:p.Asn224Tyr
  • NP_001351981.1:p.Asn176Tyr
  • NP_001373231.1:p.Asn224Tyr
  • NP_001373232.1:p.Asn251Tyr
  • NP_001373233.1:p.Asn224Tyr
  • NP_001373234.1:p.Asn224Tyr
  • NP_001373235.1:p.Asn152Tyr
  • LRG_577t1:c.670A>T
  • LRG_577:g.11533A>T
  • LRG_577p1:p.Asn224Tyr
  • NC_000001.10:g.173879984T>A
  • NM_000488.3:c.670A>T
Protein change:
N152Y
Links:
dbSNP: rs146733468
NCBI 1000 Genomes Browser:
rs146733468
Molecular consequence:
  • NM_000488.4:c.670A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365052.2:c.526A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386302.1:c.670A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386303.1:c.751A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386304.1:c.670A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386305.1:c.670A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386306.1:c.454A>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001190104MVZ Dr. Eberhard & Partner Dortmund
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Sep 18, 2019)
unknownclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknown1not providednot provided1not providedclinical testing

Citations

PubMed

Sequence, phylogenetic and variant analyses of antithrombin III.

Kumar A, Bhandari A, Sarde SJ, Goswami C.

Biochem Biophys Res Commun. 2013 Nov 1;440(4):714-24. doi: 10.1016/j.bbrc.2013.09.134. Epub 2013 Oct 9.

PubMed [citation]
PMID:
24121110

Role of the C-sheet in the maturation of N-glycans on antithrombin: functional relevance of pleiotropic mutations.

Aguila S, Navarro-Fernández J, Bohdan N, Gutiérrez-Gallego R, de la Morena-Barrio ME, Vicente V, Corral J, Martínez-Martínez I.

J Thromb Haemost. 2014 Jul;12(7):1131-40. doi: 10.1111/jth.12606. Epub 2014 Jun 19.

PubMed [citation]
PMID:
24824609
See all PubMed Citations (3)

Details of each submission

From MVZ Dr. Eberhard & Partner Dortmund, SCV001190104.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing
(GTR000327579.2)
PubMed (3)

Description

c.670A>Tfor p.(Asn224Tyr) is absent from controls like ESP, 1000 genomes or gnomAD. Multiple lines of computational evidence support a deleterious effect of this variant (SIFT: not tolerated; Mutation Taster: diesease causing; Polyphen: HumDiv and HumVar: probably damaging, large physicochemical difference between Asn and Tyr, Grantham dist.: 143 [0-215]). Asn224 is a highly conserverd amino acid and one of four N-glycosylation sites of the antithrombin molecule (Águila et al., Throm Haemost 12(7):1131-40, 2014 and Kumar et al., Biochem Biophys Res Commun 440(4):714-724, 2013). In silico analyses give no hint that this variant affects splicing.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknown1not providednot provided
(GTR000327579.2)
1not providednot providednot provided

Last Updated: Jun 23, 2024