NM_002318.3(LOXL2):c.598C>A (p.Pro200Thr) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 11, 2022
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:: RCV004151210.1

Allele description [Variation Report for NM_002318.3(LOXL2):c.598C>A (p.Pro200Thr)]

NM_002318.3(LOXL2):c.598C>A (p.Pro200Thr)

Genes:

LOXL2-AS1:LOXL2 antisense RNA 1 [Gene - HGNC]
LOXL2:lysyl oxidase like 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8p21.3

Genomic location:

Preferred name:

NM_002318.3(LOXL2):c.598C>A (p.Pro200Thr)

HGVS:

NC_000008.11:g.23341137G>T
NM_002318.3:c.598C>AMANE SELECT
NP_002309.1:p.Pro200Thr
NC_000008.10:g.23198650G>T
NM_002318.2:c.598C>A
NR_038323.1:n.1362G>T

Protein change:

P200T

Molecular consequence:

NM_002318.3:c.598C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_038323.1:n.1362G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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PRAME family member 10 [Homo sapiens]
PRAME family member 10 [Homo sapiens]
gi|85567267|gb|AAI12211.1|

Protein
NADH dehydrogenase subunit 2, partial (mitochondrion) [Melloria quoyi]
NADH dehydrogenase subunit 2, partial (mitochondrion) [Melloria quoyi]
gi|411147910|gb|AEV46411.3|

Protein
Homo sapiens BRCA2 and CDKN1A interacting protein (BCCIP), RefSeqGene on chromos...
Homo sapiens BRCA2 and CDKN1A interacting protein (BCCIP), RefSeqGene on chromosome 10
gi|335892833|ref|NG_029095.1|

Nucleotide
Epinephelini recombination activating protein 1 (RAG1) gene, partial cds.
Epinephelini recombination activating protein 1 (RAG1) gene, partial cds.
PopSet: 896682426

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003642312	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 11, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003642312

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 11, 2022)

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

Details of each submission

From Ambry Genetics, SCV003642312.2

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

Description

The c.598C>A (p.P200T) alteration is located in exon 4 (coding exon 3) of the LOXL2 gene. This alteration results from a C to A substitution at nucleotide position 598, causing the proline (P) at amino acid position 200 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: Nov 10, 2024

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