GeneBe

rs59164738

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001278689.2(EOGT):​c.*289_*293delTTTTT variant causes a 3 prime UTR change involving the alteration of a non-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: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

EOGT
NM_001278689.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.904

Publications

1 publications found
Variant links:
Genes affected
EOGT (HGNC:28526): (EGF domain specific O-linked N-acetylglucosamine transferase) This gene encodes an enzyme that acts in the lumen of the endoplasmic reticulum to catalyze the transfer of N-acetylglucosamine to serine or threonine residues of extracellular-targeted proteins. This enzyme modifies proteins containing eukaryotic growth factor (EGF)-like domains, including the Notch receptor, thereby regulating developmental signalling. Mutations in this gene have been observed in individuals with Adams-Oliver syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
EOGT Gene-Disease associations (from GenCC):
  • Adams-Oliver syndrome 4
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
  • Adams-Oliver syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278689.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EOGT
NM_001278689.2
MANE Select
c.*289_*293delTTTTT
3_prime_UTR
Exon 18 of 18NP_001265618.1Q5NDL2-1
EOGT
NM_173654.3
c.*289_*293delTTTTT
3_prime_UTR
Exon 15 of 15NP_775925.1Q5NDL2-3
EOGT
NR_103826.2
n.2128_2132delTTTTT
non_coding_transcript_exon
Exon 16 of 16

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EOGT
ENST00000383701.8
TSL:1 MANE Select
c.*289_*293delTTTTT
3_prime_UTR
Exon 18 of 18ENSP00000373206.3Q5NDL2-1
EOGT
ENST00000295571.9
TSL:1
c.*289_*293delTTTTT
3_prime_UTR
Exon 15 of 15ENSP00000295571.5Q5NDL2-3
EOGT
ENST00000403140.6
TSL:2
n.*1041_*1045delTTTTT
non_coding_transcript_exon
Exon 16 of 16ENSP00000384124.2F5H225

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
63246
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
33822
African (AFR)
AF:
0.00
AC:
0
AN:
808
American (AMR)
AF:
0.00
AC:
0
AN:
772
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1724
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1362
South Asian (SAS)
AF:
0.00
AC:
0
AN:
8916
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3688
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
42028
Other (OTH)
AF:
0.00
AC:
0
AN:
3656
GnomAD4 genome
Cov.:
30
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.90

Splicing

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

Publications

Other links and lift over

dbSNP: rs59164738; hg19: chr3-69026475; API