NM_000295.5(SERPINA1):c.701T>A (p.Val234Glu) AND Alpha-1-antitrypsin deficiency

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Nov 30, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000314851.8

Allele description [Variation Report for NM_000295.5(SERPINA1):c.701T>A (p.Val234Glu)]

NM_000295.5(SERPINA1):c.701T>A (p.Val234Glu)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

14q32.13

Genomic location:

Preferred name:

NM_000295.5(SERPINA1):c.701T>A (p.Val234Glu)

HGVS:

NC_000014.9:g.94381087A>T
NG_008290.1:g.14606T>A
NM_000295.5:c.701T>AMANE SELECT
NM_001002235.3:c.701T>A
NM_001002236.3:c.701T>A
NM_001127700.2:c.701T>A
NM_001127701.2:c.701T>A
NM_001127702.2:c.701T>A
NM_001127703.2:c.701T>A
NM_001127704.2:c.701T>A
NM_001127705.2:c.701T>A
NM_001127706.2:c.701T>A
NM_001127707.2:c.701T>A
NP_000286.3:p.Val234Glu
NP_001002235.1:p.Val234Glu
NP_001002236.1:p.Val234Glu
NP_001121172.1:p.Val234Glu
NP_001121173.1:p.Val234Glu
NP_001121174.1:p.Val234Glu
NP_001121175.1:p.Val234Glu
NP_001121176.1:p.Val234Glu
NP_001121177.1:p.Val234Glu
NP_001121178.1:p.Val234Glu
NP_001121179.1:p.Val234Glu
LRG_575t1:c.701T>A
LRG_575:g.14606T>A
LRG_575p1:p.Val234Glu
NC_000014.8:g.94847424A>T
NM_000295.4:c.701T>A

Protein change:

V234E

Links:

dbSNP: rs746197812

NCBI 1000 Genomes Browser:

rs746197812

Molecular consequence:

NM_000295.5:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001002235.3:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001002236.3:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127700.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127701.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127702.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127703.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127704.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127705.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127706.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127707.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Alpha-1-antitrypsin deficiency (A1ATD)
Synonyms:: AAT deficiency; A1AT deficiency; Alpha1-Antitrypsin Deficiency
Identifiers:: MONDO: MONDO:0013282; MedGen: C0221757; Orphanet: 60; OMIM: 613490

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000389652	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV002789017	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 15, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004203141	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 30, 2022)	unknown	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

SCV000389652

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV002789017

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 15, 2022)

unknown

clinical testing

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

SCV004203141

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 30, 2022)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000389652.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002789017.1

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

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

From Baylor Genetics, SCV004203141.1

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

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

Last Updated: Feb 4, 2024

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