NM_006031.6:c.6888G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006031.6(PCNT):c.6888G>A(p.Pro2296Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000111 in 1,446,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P2296P) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
PCNT
NM_006031.6 synonymous
NM_006031.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.53
Publications
0 publications found
Genes affected
PCNT (HGNC:16068): (pericentrin) The protein encoded by this gene binds to calmodulin and is expressed in the centrosome. It is an integral component of the pericentriolar material (PCM). The protein contains a series of coiled-coil domains and a highly conserved PCM targeting motif called the PACT domain near its C-terminus. The protein interacts with the microtubule nucleation component gamma-tubulin and is likely important to normal functioning of the centrosomes, cytoskeleton, and cell-cycle progression. Mutations in this gene cause Seckel syndrome-4 and microcephalic osteodysplastic primordial dwarfism type II. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
PCNT Gene-Disease associations (from GenCC):
- microcephalic osteodysplastic primordial dwarfism type IIInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
- Moyamoya diseaseInheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 21-46416806-G-A is Benign according to our data. Variant chr21-46416806-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 436213.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.53 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_006031.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PCNT | NM_006031.6 | MANE Select | c.6888G>A | p.Pro2296Pro | synonymous | Exon 30 of 47 | NP_006022.3 | ||
| PCNT | NM_001315529.2 | c.6534G>A | p.Pro2178Pro | synonymous | Exon 30 of 47 | NP_001302458.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PCNT | ENST00000359568.10 | TSL:1 MANE Select | c.6888G>A | p.Pro2296Pro | synonymous | Exon 30 of 47 | ENSP00000352572.5 | ||
| PCNT | ENST00000480896.5 | TSL:1 | c.6534G>A | p.Pro2178Pro | synonymous | Exon 30 of 47 | ENSP00000511989.1 | ||
| PCNT | ENST00000695558.1 | c.6921G>A | p.Pro2307Pro | synonymous | Exon 31 of 48 | ENSP00000512015.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000304 AC: 7AN: 229996 AF XY: 0.0000472 show subpopulations
GnomAD2 exomes
AF:
AC:
7
AN:
229996
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000111 AC: 16AN: 1446606Hom.: 0 Cov.: 34 AF XY: 0.0000139 AC XY: 10AN XY: 720040 show subpopulations
GnomAD4 exome
AF:
AC:
16
AN:
1446606
Hom.:
Cov.:
34
AF XY:
AC XY:
10
AN XY:
720040
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33446
American (AMR)
AF:
AC:
2
AN:
44632
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26090
East Asian (EAS)
AF:
AC:
3
AN:
39684
South Asian (SAS)
AF:
AC:
5
AN:
86136
European-Finnish (FIN)
AF:
AC:
0
AN:
39552
Middle Eastern (MID)
AF:
AC:
0
AN:
5446
European-Non Finnish (NFE)
AF:
AC:
5
AN:
1111426
Other (OTH)
AF:
AC:
1
AN:
60194
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.481
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
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EpiCase
AF:
EpiControl
AF:
ClinVar
ClinVar submissions as Germline
Significance:Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
-
-
1
not specified (1)
-
-
1
PCNT-related disorder (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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