rs1057517407

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The ENST00000222214.10(GCDH):​c.873del​(p.Asn291LysfsTer41) 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 Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. N291N) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

GCDH
ENST00000222214.10 frameshift

Scores

Not classified

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 1.95
Variant links:
Genes affected
GCDH (HGNC:4189): (glutaryl-CoA dehydrogenase) The protein encoded by this gene belongs to the acyl-CoA dehydrogenase family. It catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and CO(2) in the degradative pathway of L-lysine, L-hydroxylysine, and L-tryptophan metabolism. It uses electron transfer flavoprotein as its electron acceptor. The enzyme exists in the mitochondrial matrix as a homotetramer of 45-kD subunits. Mutations in this gene result in the metabolic disorder glutaric aciduria type 1, which is also known as glutaric acidemia type I. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 12. [provided by RefSeq, Mar 2013]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 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 19-12896929-AC-A is Pathogenic according to our data. Variant chr19-12896929-AC-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 371609.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-12896929-AC-A is described in Lovd as [Pathogenic]. Variant chr19-12896929-AC-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GCDHNM_000159.4 linkuse as main transcriptc.873del p.Asn291LysfsTer41 frameshift_variant 9/12 ENST00000222214.10 NP_000150.1
GCDHNM_013976.5 linkuse as main transcriptc.873del p.Asn291LysfsTer41 frameshift_variant 9/12 NP_039663.1
GCDHNR_102316.1 linkuse as main transcriptn.1036del non_coding_transcript_exon_variant 9/12
GCDHNR_102317.1 linkuse as main transcriptn.1254del non_coding_transcript_exon_variant 8/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GCDHENST00000222214.10 linkuse as main transcriptc.873del p.Asn291LysfsTer41 frameshift_variant 9/121 NM_000159.4 ENSP00000222214 P1Q92947-1

Frequencies

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

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Glutaric aciduria, type 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingCounsylOct 31, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

LitVar

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

Other links and lift over

dbSNP: rs1057517407; hg19: chr19-13007743; API