NM_001040716.2:c.3462G>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1

The NM_001040716.2(PC):c.3462G>C(p.Glu1154Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. E1154E) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000010 ( 0 hom. )

Consequence

PC
NM_001040716.2 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:1

Conservation

PhyloP100: -0.118

Publications

0 publications found

Variant links:

Genes affected

PC (HGNC:8636): (pyruvate carboxylase) This gene encodes pyruvate carboxylase, which requires biotin and ATP to catalyse the carboxylation of pyruvate to oxaloacetate. The active enzyme is a homotetramer arranged in a tetrahedron which is located exclusively in the mitochondrial matrix. Pyruvate carboxylase is involved in gluconeogenesis, lipogenesis, insulin secretion and synthesis of the neurotransmitter glutamate. Mutations in this gene have been associated with pyruvate carboxylase deficiency. Alternatively spliced transcript variants with different 5' UTRs, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

PC Gene-Disease associations (from GenCC):

pyruvate carboxylase deficiency disease
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Myriad Women’s Health, Labcorp Genetics (formerly Invitae), G2P
pyruvate carboxylase deficiency, benign type
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
pyruvate carboxylase deficiency, infantile form
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
pyruvate carboxylase deficiency, severe neonatal type
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

PC 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 (MetaRNN=0.031395108).

BP6

Variant 11-66848974-C-G is Benign according to our data. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839. Variant chr11-66848974-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 570839.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00019 (29/152256) while in subpopulation AFR AF = 0.000699 (29/41466). AF 95% confidence interval is 0.000499. There are 0 homozygotes in GnomAd4. There are 13 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PC	NM_001040716.2 link	c.3462G>C	p.Glu1154Asp	missense_variant	Exon 23 of 23	ENST00000393960.7	NP_001035806.1	P11498-1A0A024R5C5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PC	ENST00000393960.7 link	c.3462G>C	p.Glu1154Asp	missense_variant	Exon 23 of 23	5	NM_001040716.2	ENSP00000377532.1		P11498-1

Frequencies

GnomAD3 genomes

AF:

0.000190

AC:

AN:

152256

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000699

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000398

AC:

AN:

251258

AF XY:

0.0000368

show subpopulations

Gnomad AFR exome

AF:

0.000615

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000103

AC:

AN:

1461746

Hom.:

Cov.:

AF XY:

0.00000963

AC XY:

AN XY:

727174

show subpopulations

African (AFR)

AF:

0.000418

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53276

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1112010

Other (OTH)

AF:

0.0000166

AC:

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.000190

AC:

AN:

152256

Hom.:

Cov.:

AF XY:

0.000175

AC XY:

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.000699

AC:

AN:

41466

American (AMR)

AF:

0.00

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5200

South Asian (SAS)

AF:

0.00

AC:

AN:

4838

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68038

Other (OTH)

AF:

0.00

AC:

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

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:

0.0000434

Hom.:

Bravo

AF:

0.000189

ESP6500AA

AF:

0.000682

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.0000659

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:2Benign:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Inborn genetic diseases

Uncertain:1

Apr 24, 2025

Ambry Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.3462G>C (p.E1154D) alteration is located in exon 22 (coding exon 20) of the PC gene. This alteration results from a G to C substitution at nucleotide position 3462, causing the glutamic acid (E) at amino acid position 1154 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

not provided

Uncertain:1

Mar 07, 2025

GeneDx

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Pyruvate carboxylase deficiency

Benign:1

Feb 25, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.39

CADD

Benign

(source)

DANN

Benign

0.76

DEOGEN2

Benign

0.0053

T;T;T;T

Eigen

Benign

-0.91

Eigen_PC

Benign

-0.62

FATHMM_MKL

Benign

0.49

LIST_S2

Benign

0.72

.;.;.;T

M_CAP

Benign

0.012

MetaRNN

Benign

0.031

T;T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

-2.0

.;N;N;N

PhyloP100

-0.12

PrimateAI

Benign

0.38

PROVEAN

Benign

0.35

N;N;N;N

REVEL

Benign

0.20

Sift

Benign

0.62

T;T;T;T

Sift4G

Benign

1.0

T;T;T;T

Polyphen

0.0

.;B;B;B

Vest4

0.089

MutPred

0.35

.;Loss of methylation at K1159 (P = 0.1309);Loss of methylation at K1159 (P = 0.1309);Loss of methylation at K1159 (P = 0.1309);

MVP

0.31

MPC

0.37

ClinPred

0.028

GERP RS

2.8

Varity_R

0.13

Mutation Taster

=87/13

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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