rs1554327284

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5

The NM_001129.5(AEBP1):​c.1320_1326del​(p.Arg440SerfsTer3) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)

Consequence

AEBP1
NM_001129.5 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 3.05
Variant links:
Genes affected
AEBP1 (HGNC:303): (AE binding protein 1) This gene encodes a member of carboxypeptidase A protein family. The encoded protein may function as a transcriptional repressor and play a role in adipogenesis and smooth muscle cell differentiation. Studies in mice suggest that this gene functions in wound healing and abdominal wall development. Overexpression of this gene is associated with glioblastoma. [provided by RefSeq, May 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 7-44110261-GCCAGGAC-G is Pathogenic according to our data. Variant chr7-44110261-GCCAGGAC-G is described in ClinVar as [Pathogenic]. Clinvar id is 545024.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr7-44110261-GCCAGGAC-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AEBP1NM_001129.5 linkuse as main transcriptc.1320_1326del p.Arg440SerfsTer3 frameshift_variant 11/21 ENST00000223357.8
AEBP1XM_011515162.2 linkuse as main transcriptc.1242_1248del p.Arg414SerfsTer3 frameshift_variant 10/20

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AEBP1ENST00000223357.8 linkuse as main transcriptc.1320_1326del p.Arg440SerfsTer3 frameshift_variant 11/211 NM_001129.5 P1Q8IUX7-1
AEBP1ENST00000434445.1 linkuse as main transcript p.Arg1SerfsTer? coding_sequence_variant, 5_prime_UTR_variant, NMD_transcript_variant 1/45
AEBP1ENST00000453052.1 linkuse as main transcript downstream_gene_variant 3

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Ehlers-Danlos syndrome, classic-like, 2 Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMMay 30, 2018- -

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: rs1554327284; hg19: chr7-44149860; API