NM_005768.6(LPCAT3):c.1379T>C (p.Ile460Thr) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 29, 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:: RCV004410560.1

Allele description [Variation Report for NM_005768.6(LPCAT3):c.1379T>C (p.Ile460Thr)]

NM_005768.6(LPCAT3):c.1379T>C (p.Ile460Thr)

Genes:

EMG1:EMG1 N1-specific pseudouridine methyltransferase [Gene - OMIM - HGNC]
LPCAT3:lysophosphatidylcholine acyltransferase 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p13.31

Genomic location:

Preferred name:

NM_005768.6(LPCAT3):c.1379T>C (p.Ile460Thr)

HGVS:

NC_000012.12:g.6977231A>G
NG_021408.2:g.11451A>G
NM_001320049.2:c.*1422A>G
NM_005768.6:c.1379T>CMANE SELECT
NM_006331.8:c.*1422A>GMANE SELECT
NP_005759.4:p.Ile460Thr
NC_000012.11:g.7086393A>G
NM_005768.5:c.1379T>C

Protein change:

I460T

Molecular consequence:

NM_001320049.2:c.*1422A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_006331.8:c.*1422A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_005768.6:c.1379T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004896955	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 29, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004896955

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 29, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV004896955.1

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

Description

The c.1379T>C (p.I460T) alteration is located in exon 12 (coding exon 12) of the LPCAT3 gene. This alteration results from a T to C substitution at nucleotide position 1379, causing the isoleucine (I) at amino acid position 460 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: Sep 1, 2024

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