14-36662090-A-G
Position:
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1PS1_ModeratePM2PP5
The NM_001372076.1(PAX9):āc.1A>Gā(p.Met1?) variant causes a start lost change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PAX9
NM_001372076.1 start_lost
NM_001372076.1 start_lost
Scores
7
6
3
Clinical Significance
Conservation
PhyloP100: 5.46
Genes affected
PAX9 (HGNC:8623): (paired box 9) This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. Mice lacking this gene exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and neonatal lethality. Mutations in the human gene are associated with selective tooth agenesis-3. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 13 ACMG points.
PVS1
Start lost variant, no new inframe start found.
PS1
Another start lost variant in NM_001372076.1 (PAX9) was described as [Pathogenic] in ClinVar as 430692
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 14-36662090-A-G is Pathogenic according to our data. Variant chr14-36662090-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 13777.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX9 | NM_001372076.1 | c.1A>G | p.Met1? | start_lost | 1/4 | ENST00000361487.7 | |
PAX9 | NM_006194.4 | c.1A>G | p.Met1? | start_lost | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX9 | ENST00000361487.7 | c.1A>G | p.Met1? | start_lost | 1/4 | 1 | NM_001372076.1 | P1 | |
PAX9 | ENST00000402703.6 | c.1A>G | p.Met1? | start_lost | 2/5 | 5 | P1 | ||
PAX9 | ENST00000555639.2 | c.1A>G | p.Met1? | start_lost | 2/3 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1169392Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 574120
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1169392
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
574120
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Tooth agenesis, selective, 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2005 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Pathogenic
D
MutationTaster
Benign
D;D
PROVEAN
Benign
N;N
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
B;B
Vest4
MutPred
Loss of disorder (P = 0.1886);Loss of disorder (P = 0.1886);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
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
No publications associated with this variant yet.