NM_000030.3(AGXT):c.40dup (p.Leu14fs) AND Primary hyperoxaluria, type I

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 27, 2023
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:: RCV003468699.1

Allele description [Variation Report for NM_000030.3(AGXT):c.40dup (p.Leu14fs)]

NM_000030.3(AGXT):c.40dup (p.Leu14fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

2q37.3

Genomic location:

Preferred name:

NM_000030.3(AGXT):c.40dup (p.Leu14fs)

Other names:

c.40_41insC

HGVS:

NC_000002.12:g.240868905dup
NG_008005.1:g.5161dup
NG_098313.1:g.663dup
NM_000030.3:c.40dupMANE SELECT
NP_000021.1:p.Leu14fs
NC_000002.11:g.241808322dup
NM_000030.2:c.40dup

Protein change:

L14fs

Molecular consequence:

NM_000030.3:c.40dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Primary hyperoxaluria, type I (HP1)
Synonyms:: OXALOSIS I; Primary hyperoxaluria type 1; Oxalosis 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009823; MedGen: C0268164; Orphanet: 416; Orphanet: 93598; OMIM: 259900

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Rete Testis
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MeSH
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004217806	Clinical Biochemistry Laboratory, Health Services Laboratory	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 27, 2023)	germline	curation	PubMed (2) [See all records that cite these PMIDs] 36185032, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004217806

Clinical Biochemistry Laboratory, Health Services Laboratory

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 27, 2023)

germline

curation

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	yes	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Primary hyperoxaluria: Comprehensive mutation screening of the disease causing genes and spectrum of disease-associated pathogenic variants.

Abid A, Raza A, Khan AR, Firasat S, Shahid S, Hashmi S, Zafar MN, Sultan S, Khaliq S, Rizvi SA.

Clin Genet. 2023 Jan;103(1):53-66. doi: 10.1111/cge.14240. Epub 2022 Oct 9.

PubMed [citation]

PMID:: 36185032

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 Clinical Biochemistry Laboratory, Health Services Laboratory, SCV004217806.1

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

Description

ACMG:PVS1 PM2 PM3

#	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

Last Updated: Dec 30, 2023

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