NM_004744.5(LRAT):c.163C>G (p.Arg55Gly) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 16, 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:: RCV001858668.4

Allele description [Variation Report for NM_004744.5(LRAT):c.163C>G (p.Arg55Gly)]

NM_004744.5(LRAT):c.163C>G (p.Arg55Gly)

Gene:

LRAT:lecithin retinol acyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q32.1

Genomic location:

Preferred name:

NM_004744.5(LRAT):c.163C>G (p.Arg55Gly)

HGVS:

NC_000004.12:g.154744489C>G
NG_009110.1:g.5479C>G
NM_001301645.2:c.163C>G
NM_004744.5:c.163C>GMANE SELECT
NP_001288574.1:p.Arg55Gly
NP_004735.2:p.Arg55Gly
NC_000004.11:g.155665641C>G

Protein change:

R55G

Links:

dbSNP: rs527236079

NCBI 1000 Genomes Browser:

rs527236079

Molecular consequence:

NM_001301645.2:c.163C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004744.5:c.163C>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002220849	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 16, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25324289, 29844330, 30190494, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002220849

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 16, 2023)

germline

clinical testing

PubMed (4)
[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

Comprehensive molecular diagnosis of a large cohort of Japanese retinitis pigmentosa and Usher syndrome patients by next-generation sequencing.

Oishi M, Oishi A, Gotoh N, Ogino K, Higasa K, Iida K, Makiyama Y, Morooka S, Matsuda F, Yoshimura N.

Invest Ophthalmol Vis Sci. 2014 Oct 16;55(11):7369-75. doi: 10.1167/iovs.14-15458.

PubMed [citation]

PMID:: 25324289

Molecular Diagnosis of 34 Japanese Families with Leber Congenital Amaurosis Using Targeted Next Generation Sequencing.

Hosono K, Nishina S, Yokoi T, Katagiri S, Saitsu H, Kurata K, Miyamichi D, Hikoya A, Mizobuchi K, Nakano T, Minoshima S, Fukami M, Kondo H, Sato M, Hayashi T, Azuma N, Hotta Y.

Sci Rep. 2018 May 29;8(1):8279. doi: 10.1038/s41598-018-26524-z.

PubMed [citation]

PMID:: 29844330
PMCID:: PMC5974356

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002220849.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

ClinVar contains an entry for this variant (Variation ID: 802096). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant disrupts the p.Arg55 amino acid residue in LRAT. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 25324289, 29844330). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. This missense change has been observed in individuals with inherited retinal dystrophy (PMID: 30190494; Invitae). This variant is present in population databases (no rsID available, gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 55 of the LRAT protein (p.Arg55Gly).

#	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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