NM_000488.4(SERPINC1):c.116T>A (p.Ile39Asn) AND Hereditary antithrombin deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 1, 1996
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000019637.24

Allele description [Variation Report for NM_000488.4(SERPINC1):c.116T>A (p.Ile39Asn)]

NM_000488.4(SERPINC1):c.116T>A (p.Ile39Asn)

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.116T>A (p.Ile39Asn)

Other names:

I7N

HGVS:

NC_000001.11:g.173914845A>T
NG_012462.1:g.7534T>A
NM_000488.4:c.116T>AMANE SELECT
NM_001365052.2:c.-29T>A
NM_001386302.1:c.116T>A
NM_001386303.1:c.197T>A
NM_001386304.1:c.116T>A
NM_001386305.1:c.116T>A
NM_001386306.1:c.116T>A
NP_000479.1:p.Ile39Asn
NP_001373231.1:p.Ile39Asn
NP_001373232.1:p.Ile66Asn
NP_001373233.1:p.Ile39Asn
NP_001373234.1:p.Ile39Asn
NP_001373235.1:p.Ile39Asn
LRG_577:g.7534T>A
NC_000001.10:g.173883983A>T
P01008:p.Ile39Asn

Protein change:

I39N; ILE7ASN

Links:

UniProtKB: P01008#VAR_007033; OMIM: 107300.0023; dbSNP: rs121909558

NCBI 1000 Genomes Browser:

rs121909558

Molecular consequence:

NM_001365052.2:c.-29T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000488.4:c.116T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386302.1:c.116T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386303.1:c.197T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386304.1:c.116T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386305.1:c.116T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386306.1:c.116T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary antithrombin deficiency (AT3D)
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
SCV000039935	OMIM	no assertion criteria provided	Pathogenic (Jan 1, 1996)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 3169232, 2615648

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000039935

OMIM

no assertion criteria provided

Pathogenic
(Jan 1, 1996)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

New carbohydrate site in mutant antithrombin (7 Ile----Asn) with decreased heparin affinity.

Brennan SO, Borg JY, George PM, Soria C, Soria J, Caen J, Carrell RW.

FEBS Lett. 1988 Sep 12;237(1-2):118-22.

PubMed [citation]

PMID:: 3169232

CpG dinucleotides are "hotspots" for mutation in the antithrombin III gene. Twelve variants identified using the polymerase chain reaction.

Perry DJ, Carrell RW.

Mol Biol Med. 1989 Jun;6(3):239-43.

PubMed [citation]

PMID:: 2615648

Details of each submission

From OMIM, SCV000039935.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

Brennan et al. (1988) demonstrated a substitution of asparagine for isoleucine at position 7 in a mutant antithrombin III, designated AT-III Rouen III, isolated from the plasma of a patient with pulmonary embolism (613118). The mutation introduced a new asn-cys-thr glycosylation sequence. The new oligosaccharide attachment site occupied the base of the presumed heparin-binding site, and the finding explained the consequent decrease in heparin affinity. Perry and Carrell (1989) also found this substitution, which was due to an ATC-to-AAC change, as the basis of a molecule defective in heparin binding.

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

Last Updated: Oct 8, 2024

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