rs768255532

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM5

The NM_004744.5(LRAT):​c.40G>A​(p.Glu14Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E14L) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

LRAT
NM_004744.5 missense

Scores

12
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.33
Variant links:
Genes affected
LRAT (HGNC:6685): (lecithin retinol acyltransferase) The protein encoded by this gene localizes to the endoplasmic reticulum, where it catalyzes the esterification of all-trans-retinol into all-trans-retinyl ester. This reaction is an important step in vitamin A metabolism in the visual system. Mutations in this gene have been associated with early-onset severe retinal dystrophy and Leber congenital amaurosis 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM1
In a topological_domain Cytoplasmic (size 193) in uniprot entity LRAT_HUMAN there are 15 pathogenic changes around while only 3 benign (83%) in NM_004744.5
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr4-154744365-GGA-GTT is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LRATNM_004744.5 linkc.40G>A p.Glu14Lys missense_variant Exon 2 of 3 ENST00000336356.4 NP_004735.2 O95237
LRATNM_001301645.2 linkc.40G>A p.Glu14Lys missense_variant Exon 2 of 3 NP_001288574.1 O95237
LRATXM_047416405.1 linkc.40G>A p.Glu14Lys missense_variant Exon 2 of 3 XP_047272361.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LRATENST00000336356.4 linkc.40G>A p.Glu14Lys missense_variant Exon 2 of 3 1 NM_004744.5 ENSP00000337224.3 O95237

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000796
AC:
2
AN:
251394
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135902
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1461868
Hom.:
0
Cov.:
31
AF XY:
0.00000275
AC XY:
2
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
ExAC
AF:
0.0000165
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.24
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.24
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.56
.;D;D
Eigen
Uncertain
0.30
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.82
T;.;T
M_CAP
Benign
0.072
D
MetaRNN
Uncertain
0.50
T;T;T
MetaSVM
Benign
-0.67
T
MutationAssessor
Uncertain
2.4
.;M;M
PrimateAI
Uncertain
0.51
T
PROVEAN
Uncertain
-3.1
D;N;N
REVEL
Uncertain
0.32
Sift
Uncertain
0.0080
D;D;D
Sift4G
Uncertain
0.0090
D;D;D
Polyphen
0.98
.;D;D
Vest4
0.52
MutPred
0.48
Gain of ubiquitination at E14 (P = 0.023);Gain of ubiquitination at E14 (P = 0.023);Gain of ubiquitination at E14 (P = 0.023);
MVP
0.71
MPC
1.3
ClinPred
0.97
D
GERP RS
4.4
Varity_R
0.14
gMVP
0.91

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs768255532; hg19: chr4-155665518; API