17-35132441-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018096.5(NLE1):c.1454G>A(p.Arg485Lys) 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018096.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLE1 | NM_018096.5 | c.1454G>A | p.Arg485Lys | missense_variant | Exon 13 of 13 | ENST00000442241.9 | NP_060566.2 | |
NLE1 | NM_001014445.2 | c.578G>A | p.Arg193Lys | missense_variant | Exon 12 of 12 | NP_001014445.1 | ||
NLE1 | XM_017024777.2 | c.578G>A | p.Arg193Lys | missense_variant | Exon 11 of 11 | XP_016880266.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NLE1 | ENST00000442241.9 | c.1454G>A | p.Arg485Lys | missense_variant | Exon 13 of 13 | 1 | NM_018096.5 | ENSP00000413572.3 | ||
NLE1 | ENST00000586869.5 | c.578G>A | p.Arg193Lys | missense_variant | Exon 12 of 12 | 1 | ENSP00000466588.1 | |||
NLE1 | ENST00000360831.9 | c.1328G>A | p.Arg443Lys | missense_variant | Exon 12 of 12 | 5 | ENSP00000354075.5 | |||
NLE1 | ENST00000588019.1 | c.908G>A | p.Arg303Lys | missense_variant | Exon 8 of 8 | 5 | ENSP00000466764.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1454G>A (p.R485K) alteration is located in exon 13 (coding exon 13) of the NLE1 gene. This alteration results from a G to A substitution at nucleotide position 1454, causing the arginine (R) at amino acid position 485 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.