NM_001127701.1(SERPINA1):c.187C>T (p.Arg63Cys) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Apr 1, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000431149.26

Allele description

NM_001127701.1(SERPINA1):c.187C>T (p.Arg63Cys)

Gene:

SERPINA1:serpin family A member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q32.13

Genomic location:

Preferred name:

NM_001127701.1(SERPINA1):c.187C>T (p.Arg63Cys)

Other names:

R39C; SERPINA1, ARG39CYS ON M1V

HGVS:

NC_000014.9:g.94383051G>A
NG_008290.1:g.12642C>T
NM_000295.5:c.187C>TMANE SELECT
NM_001002235.3:c.187C>T
NM_001002236.3:c.187C>T
NM_001127700.2:c.187C>T
NM_001127701.2:c.187C>T
NM_001127702.2:c.187C>T
NM_001127703.2:c.187C>T
NM_001127704.2:c.187C>T
NM_001127705.2:c.187C>T
NM_001127706.2:c.187C>T
NM_001127707.2:c.187C>T
NP_000286.3:p.Arg63Cys
NP_001002235.1:p.Arg63Cys
NP_001002236.1:p.Arg63Cys
NP_001121172.1:p.Arg63Cys
NP_001121173.1:p.Arg63Cys
NP_001121174.1:p.Arg63Cys
NP_001121175.1:p.Arg63Cys
NP_001121176.1:p.Arg63Cys
NP_001121177.1:p.Arg63Cys
NP_001121178.1:p.Arg63Cys
NP_001121179.1:p.Arg63Cys
LRG_575t1:c.187C>T
LRG_575:g.12642C>T
LRG_575p1:p.Arg63Cys
NC_000014.8:g.94849388G>A
NM_000295.4:c.187C>T
P01009:p.Arg63Cys

Protein change:

R63C; ARG39CYS

Links:

UniProtKB: P01009#VAR_006981; OMIM: 107400.0018; dbSNP: rs28931570

NCBI 1000 Genomes Browser:

rs28931570

Molecular consequence:

NM_000295.5:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001002235.3:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001002236.3:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127700.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127701.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127702.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127703.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127704.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127705.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127706.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127707.2:c.187C>T - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

effect on catalytic protein function [Variation Ontology: 0008]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Mus musculus heterogeneous nuclear ribonucleoprotein K (Hnrnpk), transcript vari...
Mus musculus heterogeneous nuclear ribonucleoprotein K (Hnrnpk), transcript variant 3, mRNA
gi|672424486|ref|NM_001301343.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000227088	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely pathogenic (Aug 14, 2017)	germline	clinical testing	Citation Link,
SCV000521230	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 12, 2022)	germline	clinical testing	Citation Link,
SCV001500625	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Apr 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000227088

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Likely pathogenic
(Aug 14, 2017)

germline

clinical testing

Citation Link,

SCV000521230

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 12, 2022)

germline

clinical testing

Citation Link,

SCV001500625

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Apr 1, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	4	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	16	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000227088.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	16	not provided	not provided	clinical testing	not provided

#	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		16	not provided	not provided	not provided

From GeneDx, SCV000521230.6

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

Description

Published functional studies demonstrate that the R63C variant impairs protein secretion by forming aberrant disulfide bonds (Ronzoni et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24713750, 29882371, 26987331, 24055113, 25637381, 21228398, 23632999, 27296815, 30487145, 31447099, 31589614, 2606478, 26647313, 34426522, 31980526)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001500625.19

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

Description

SERPINA1: PS3, PS4, PP4:Moderate

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		4	not provided	not provided	not provided

Last Updated: Jun 17, 2024

ClinVar

Relating variation to medicine