NM_000030.3(AGXT):c.26_27insA (p.Lys12fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 15, 2021
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:: RCV001894381.7

Allele description [Variation Report for NM_000030.3(AGXT):c.26_27insA (p.Lys12fs)]

NM_000030.3(AGXT):c.26_27insA (p.Lys12fs)

Gene:

AGXT:alanine--glyoxylate aminotransferase [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

2q37.3

Genomic location:

Preferred name:

NM_000030.3(AGXT):c.26_27insA (p.Lys12fs)

HGVS:

NC_000002.12:g.240868891_240868892insA
NG_008005.1:g.5147_5148insA
NM_000030.3:c.26_27insAMANE SELECT
NP_000021.1:p.Lys12fs
NC_000002.11:g.241808308_241808309insA

Protein change:

K12fs

Links:

dbSNP: rs2106427278

NCBI 1000 Genomes Browser:

rs2106427278

Molecular consequence:

NM_000030.3:c.26_27insA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002118413	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 15, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19479957, 15327387, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002118413

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 15, 2021)

germline

clinical testing

PubMed (3)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Primary hyperoxaluria type 1: update and additional mutation analysis of the AGXT gene.

Williams EL, Acquaviva C, Amoroso A, Chevalier F, Coulter-Mackie M, Monico CG, Giachino D, Owen T, Robbiano A, Salido E, Waterham H, Rumsby G.

Hum Mutat. 2009 Jun;30(6):910-7. doi: 10.1002/humu.21021. Review.

PubMed [citation]

PMID:: 19479957

Evaluation of mutation screening as a first line test for the diagnosis of the primary hyperoxalurias.

Rumsby G, Williams E, Coulter-Mackie M.

Kidney Int. 2004 Sep;66(3):959-63.

PubMed [citation]

PMID:: 15327387

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002118413.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Lys12Glnfs*156) in the AGXT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AGXT are known to be pathogenic (PMID: 19479957). For these reasons, this variant has been classified as Pathogenic. This frameshift ‚Äãhas been observed in individuals affected with primary hyperoxaluria (PMID: 15327387) This variant is not present in population databases (ExAC no frequency).

#	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: Sep 29, 2024

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