rs777359703

Variant names:

• chr3-136250376-ATGGCGGCGGCATTACGGG-A
• rs777359703
• NM_000532.5:c.11_28delCATTACGGGTGGCGGCGG

Your query was ambiguous. Multiple possible variants found:

• chr3-136250376-ATGGCGGCGGCATTACGGG-A
• chr3-136250376-ATGGCGGCGGCATTACGGG-ATGGCGGCGGCATTACGGGTGGCGGCGGCATTACGGG
• chr3-136250376-ATGGCGGCGGCATTACGGG-ATGGCGGCGGCATTACGGGTGGCGGCGGCATTACGGGTGGCGGCGGCATTACGGG

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.89

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]

ACMG classification

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
PCCB	NM_000532.5	c.11_28delCATTACGGGTGGCGGCGG	p.Ala4_Ala9del	disruptive_inframe_deletion	Exon 1 of 15	ENST00000251654.9	NP_000523.2
PCCB	NM_001178014.2	c.11_28delCATTACGGGTGGCGGCGG	p.Ala4_Ala9del	disruptive_inframe_deletion	Exon 1 of 16		NP_001171485.1
PCCB	XM_011512873.2	c.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
PCCB	ENST00000251654.9	c.11_28delCATTACGGGTGGCGGCGG	p.Ala4_Ala9del	disruptive_inframe_deletion	Exon 1 of 15	1	NM_000532.5	ENSP00000251654.4

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs777359703; hg19: chr3-135969218;