chr3-66380403-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015541.3(LRIG1):​c.3142G>A​(p.Glu1048Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

LRIG1
NM_015541.3 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.901
Variant links:
Genes affected
LRIG1 (HGNC:17360): (leucine rich repeats and immunoglobulin like domains 1) Predicted to act upstream of or within several processes, including innervation; otolith morphogenesis; and sensory perception of sound. Predicted to be located in plasma membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
SLC25A26 (HGNC:20661): (solute carrier family 25 member 26) This gene is a member of the mitochondrial carrier family which includes nuclear-encoded transporters localized on the inner mitochondrial membranes. Members of the family transport important small molecules across the mitochondrial inner membrane. This protein is involved in the transport of S-adenosylmethionine (SAM) into the mitochondria. Mutations in this gene are associated with combined oxidative phosphorylation deficiency 28. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2017]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08785662).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRIG1NM_015541.3 linkuse as main transcriptc.3142G>A p.Glu1048Lys missense_variant 19/19 ENST00000273261.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LRIG1ENST00000273261.8 linkuse as main transcriptc.3142G>A p.Glu1048Lys missense_variant 19/191 NM_015541.3 P1Q96JA1-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 21, 2022The c.3142G>A (p.E1048K) alteration is located in exon 19 (coding exon 19) of the LRIG1 gene. This alteration results from a G to A substitution at nucleotide position 3142, causing the glutamic acid (E) at amino acid position 1048 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.053
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
14
DANN
Benign
0.97
DEOGEN2
Benign
0.11
T;.
Eigen
Benign
-0.69
Eigen_PC
Benign
-0.78
FATHMM_MKL
Benign
0.11
N
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.088
T;T
MetaSVM
Benign
-0.88
T
MutationAssessor
Benign
2.0
M;.
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-0.69
N;N
REVEL
Benign
0.14
Sift
Uncertain
0.0080
D;D
Sift4G
Benign
0.58
T;T
Polyphen
0.10
B;P
Vest4
0.18
MutPred
0.23
Gain of ubiquitination at E1048 (P = 0.0025);.;
MVP
0.37
MPC
0.11
ClinPred
0.17
T
GERP RS
0.90
Varity_R
0.067
gMVP
0.10

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-66430827; API