2-88627211-CCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAG

Variant summary

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

The NM_004836.7(EIF2AK3):​c.55_63dupCTGCTGCTG​(p.Leu19_Leu21dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000047 ( 0 hom. )

Consequence

EIF2AK3
NM_004836.7 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.853
Variant links:
Genes affected
EIF2AK3 (HGNC:3255): (eukaryotic translation initiation factor 2 alpha kinase 3) The protein encoded by this gene phosphorylates the alpha subunit of eukaryotic translation-initiation factor 2, leading to its inactivation, and thus to a rapid reduction of translational initiation and repression of global protein synthesis. This protein is thought to modulate mitochondrial function. It is a type I membrane protein located in the endoplasmic reticulum (ER), where it is induced by ER stress caused by malfolded proteins. Mutations in this gene are associated with Wolcott-Rallison syndrome. [provided by RefSeq, Sep 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EIF2AK3NM_004836.7 linkc.55_63dupCTGCTGCTG p.Leu19_Leu21dup conservative_inframe_insertion Exon 1 of 17 ENST00000303236.9 NP_004827.4 Q9NZJ5B3KY45
EIF2AK3XM_047446430.1 linkc.55_63dupCTGCTGCTG p.Leu19_Leu21dup conservative_inframe_insertion Exon 1 of 12 XP_047302386.1
EIF2AK3XM_047446428.1 linkc.17+469_17+477dupCTGCTGCTG intron_variant Intron 1 of 16 XP_047302384.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EIF2AK3ENST00000303236.9 linkc.55_63dupCTGCTGCTG p.Leu19_Leu21dup conservative_inframe_insertion Exon 1 of 17 1 NM_004836.7 ENSP00000307235.3 Q9NZJ5
EIF2AK3ENST00000682892.1 linkc.-145-13367_-145-13359dupCTGCTGCTG intron_variant Intron 2 of 17 ENSP00000507214.1 A0A804HIT4
EIF2AK3ENST00000652099.1 linkn.52_60dupCTGCTGCTG non_coding_transcript_exon_variant Exon 1 of 18 ENSP00000498211.1 A0A494BZR8
EIF2AK3ENST00000652423.1 linkn.55_63dupCTGCTGCTG non_coding_transcript_exon_variant Exon 1 of 4 ENSP00000498948.1 A0A494C186

Frequencies

GnomAD3 genomes
AF:
0.00000662
AC:
1
AN:
151044
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000469
AC:
6
AN:
1278938
Hom.:
0
Cov.:
0
AF XY:
0.00000635
AC XY:
4
AN XY:
630080
show subpopulations
Gnomad4 AFR exome
AF:
0.0000781
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000730
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000196
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000662
AC:
1
AN:
151044
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
73738
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000148
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1805190; hg19: chr2-88926729; API