rs755282356
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000374647.10(ELP1):āc.1529A>Gā(p.Glu510Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,976 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
ENST00000374647.10 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.1529A>G | p.Glu510Gly | missense_variant | 14/37 | ENST00000374647.10 | NP_003631.2 | |
ELP1 | NM_001318360.2 | c.1187A>G | p.Glu396Gly | missense_variant | 14/37 | NP_001305289.1 | ||
ELP1 | NM_001330749.2 | c.482A>G | p.Glu161Gly | missense_variant | 12/35 | NP_001317678.1 | ||
ELP1 | XM_047423991.1 | c.1529A>G | p.Glu510Gly | missense_variant | 14/25 | XP_047279947.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELP1 | ENST00000374647.10 | c.1529A>G | p.Glu510Gly | missense_variant | 14/37 | 1 | NM_003640.5 | ENSP00000363779 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251344Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135838
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461756Hom.: 1 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727192
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 05, 2022 | This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 510 of the ELP1 protein (p.Glu510Gly). This variant is present in population databases (rs755282356, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with ELP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 526192). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Clinical Genetics Laboratory, Skane University Hospital Lund | May 27, 2022 | - - |
Familial dysautonomia Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.1529A>G (p.E510G) alteration is located in exon 14 (coding exon 13) of the IKBKAP gene. This alteration results from a A to G substitution at nucleotide position 1529, causing the glutamic acid (E) at amino acid position 510 to be replaced by a glycine (G). 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