rs777359703

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_000532.5(PCCB):​c.11_28delCATTACGGGTGGCGGCGG​(p.Ala4_Ala9del) variant causes a disruptive inframe deletion change. 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: 33)

Consequence

PCCB
NM_000532.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.89
Variant links:
Genes affected
PCCB (HGNC:8654): (propionyl-CoA carboxylase subunit beta) The protein encoded by this gene is a subunit of the propionyl-CoA carboxylase (PCC) enzyme, which is involved in the catabolism of propionyl-CoA. PCC is a mitochondrial enzyme that probably acts as a dodecamer of six alpha subunits and six beta subunits. This gene encodes the beta subunit of PCC. Defects in this gene are a cause of propionic acidemia type II (PA-2). Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_000532.5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCCBNM_000532.5 linkc.11_28delCATTACGGGTGGCGGCGG p.Ala4_Ala9del disruptive_inframe_deletion Exon 1 of 15 ENST00000251654.9 NP_000523.2 P05166-1
PCCBNM_001178014.2 linkc.11_28delCATTACGGGTGGCGGCGG p.Ala4_Ala9del disruptive_inframe_deletion Exon 1 of 16 NP_001171485.1 P05166-2
PCCBXM_011512873.2 linkc.11_28delCATTACGGGTGGCGGCGG p.Ala4_Ala9del disruptive_inframe_deletion Exon 1 of 11 XP_011511175.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCCBENST00000251654.9 linkc.11_28delCATTACGGGTGGCGGCGG p.Ala4_Ala9del disruptive_inframe_deletion Exon 1 of 15 1 NM_000532.5 ENSP00000251654.4 P05166-1

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
Bravo
AF:
0.00000378

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: rs777359703; hg19: chr3-135969218; API