rs119476044
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_022051.3(EGLN1):c.1112G>A(p.Arg371His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R371C) has been classified as Uncertain significance.
Frequency
Consequence
NM_022051.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGLN1 | NM_022051.3 | c.1112G>A | p.Arg371His | missense_variant | 3/5 | ENST00000366641.4 | NP_071334.1 | |
EGLN1 | NM_001377260.1 | c.1112G>A | p.Arg371His | missense_variant | 3/4 | NP_001364189.1 | ||
EGLN1 | NM_001377261.1 | c.1012-2962G>A | intron_variant | NP_001364190.1 | ||||
EGLN1 | XM_024447734.2 | c.1012-2962G>A | intron_variant | XP_024303502.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGLN1 | ENST00000366641.4 | c.1112G>A | p.Arg371His | missense_variant | 3/5 | 1 | NM_022051.3 | ENSP00000355601.3 | ||
ENSG00000287856 | ENST00000662216.1 | c.251G>A | p.Arg84His | missense_variant | 5/7 | ENSP00000499467.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461768Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727208
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Erythrocytosis, familial, 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 15, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at