NM_000532.5:c.429+7G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_000532.5(PCCB):c.429+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000637 in 1,607,904 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00069 ( 3 hom., cov: 33)

Exomes 𝑓: 0.00063 ( 2 hom. )

Consequence

PCCB
NM_000532.5 splice_region, intron

Scores

Splicing: ADA: 0.00005771

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:5

Conservation

PhyloP100: -0.308

Publications

0 publications found

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]

PCCB Gene-Disease associations (from GenCC):

propionic acidemia
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), G2P, ClinGen, Myriad Women’s Health, Orphanet

PCCB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 3-136260542-G-A is Benign according to our data. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463. Variant chr3-136260542-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 343463.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PCCB	NM_000532.5 link	c.429+7G>A	splice_region_variant, intron_variant	Intron 4 of 14	ENST00000251654.9	NP_000523.2	P05166-1
PCCB	NM_001178014.2 link	c.489+7G>A	splice_region_variant, intron_variant	Intron 5 of 15		NP_001171485.1	P05166-2
PCCB	XM_011512873.2 link	c.429+7G>A	splice_region_variant, intron_variant	Intron 4 of 10		XP_011511175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCCB	ENST00000251654.9 link	c.429+7G>A		splice_region_variant, intron_variant	Intron 4 of 14	1	NM_000532.5	ENSP00000251654.4		P05166-1

Frequencies

GnomAD3 genomes

AF:

0.000690

AC:

105

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00137

Gnomad OTH

AF:

0.000479

GnomAD2 exomes

AF:

0.000599

AC:

150

AN:

250496

AF XY:

0.000576

show subpopulations

Gnomad AFR exome

AF:

0.0000616

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000498

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000324

Gnomad NFE exome

AF:

0.00104

Gnomad OTH exome

AF:

0.000818

GnomAD4 exome

AF:

0.000631

AC:

919

AN:

1455680

Hom.:

Cov.:

AF XY:

0.000674

AC XY:

488

AN XY:

724424

show subpopulations

African (AFR)

AF:

0.0000599

AC:

AN:

33370

American (AMR)

AF:

0.0000224

AC:

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.000805

AC:

AN:

26072

East Asian (EAS)

AF:

0.00

AC:

AN:

39664

South Asian (SAS)

AF:

0.000442

AC:

AN:

85972

European-Finnish (FIN)

AF:

0.000393

AC:

AN:

53402

Middle Eastern (MID)

AF:

0.000524

AC:

AN:

5720

European-Non Finnish (NFE)

AF:

0.000721

AC:

798

AN:

1106626

Other (OTH)

AF:

0.000582

AC:

AN:

60178

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

139

186

232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000690

AC:

105

AN:

152224

Hom.:

Cov.:

AF XY:

0.000524

AC XY:

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0000965

AC:

AN:

41460

American (AMR)

AF:

0.00

AC:

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5200

South Asian (SAS)

AF:

0.00

AC:

AN:

4838

European-Finnish (FIN)

AF:

0.0000942

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00137

AC:

AN:

68044

Other (OTH)

AF:

0.000479

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00106

Hom.:

Bravo

AF:

0.000521

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.000927

EpiControl

AF:

0.000357

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:5

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Propionic acidemia

Uncertain:1Benign:2

Nov 11, 2019

Natera, Inc.

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:2

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 27, 2017

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Jul 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

PCCB: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.9

(source)

DANN

Benign

0.65

PhyloP100

-0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000058

dbscSNV1_RF

Benign

0.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over