ENST00000601627.1:n.118-235C>A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_080732.4(EGLN2):​c.607G>A​(p.Gly203Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

EGLN2
NM_080732.4 missense

Scores

3
7
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 8.00
Variant links:
Genes affected
EGLN2 (HGNC:14660): (egl-9 family hypoxia inducible factor 2) The hypoxia inducible factor (HIF) is a transcriptional complex that is involved in oxygen homeostasis. At normal oxygen levels, the alpha subunit of HIF is targeted for degration by prolyl hydroxylation. This gene encodes an enzyme responsible for this post-translational modification. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream RAB4B (RAB4B, member RAS oncogene family) gene. [provided by RefSeq, Feb 2011]
RAB4B-EGLN2 (HGNC:44465): (RAB4B-EGLN2 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring RAB4B (RAB4B, member RAS oncogene family) and EGLN2 (egl nine homolog 2) genes on chromosome 19. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EGLN2NM_080732.4 linkc.607G>A p.Gly203Ser missense_variant Exon 2 of 6 ENST00000303961.9 NP_542770.2 Q96KS0-1A0A024R0R2
EGLN2NM_053046.4 linkc.607G>A p.Gly203Ser missense_variant Exon 2 of 6 NP_444274.1 Q96KS0-1A0A024R0R2
RAB4B-EGLN2NR_037791.1 linkn.1655G>A non_coding_transcript_exon_variant Exon 8 of 12

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EGLN2ENST00000303961.9 linkc.607G>A p.Gly203Ser missense_variant Exon 2 of 6 1 NM_080732.4 ENSP00000307080.3 Q96KS0-1
RAB4B-EGLN2ENST00000594136.2 linkn.*856G>A non_coding_transcript_exon_variant Exon 8 of 12 2 ENSP00000469872.1
RAB4B-EGLN2ENST00000594136.2 linkn.*856G>A 3_prime_UTR_variant Exon 8 of 12 2 ENSP00000469872.1

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.75
BayesDel_addAF
Benign
-0.066
T
BayesDel_noAF
Benign
-0.33
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.70
D;D;D
Eigen
Uncertain
0.27
Eigen_PC
Benign
0.17
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.87
.;.;D
M_CAP
Benign
0.039
D
MetaRNN
Uncertain
0.70
D;D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N;N;N
PrimateAI
Uncertain
0.60
T
PROVEAN
Pathogenic
-5.6
D;D;.
REVEL
Benign
0.21
Sift
Benign
0.031
D;D;.
Sift4G
Uncertain
0.029
D;D;D
Polyphen
0.78
P;P;P
Vest4
0.61
MutPred
0.55
Gain of phosphorylation at G203 (P = 0.0711);Gain of phosphorylation at G203 (P = 0.0711);Gain of phosphorylation at G203 (P = 0.0711);
MVP
0.69
MPC
1.3
ClinPred
0.97
D
GERP RS
3.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6
Varity_R
0.57
gMVP
0.89

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: chr19-41307084; API