X-69162074-T-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001032396.4(PJA1):āc.1000A>Gā(p.Ser334Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000629 in 1,208,916 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 26 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00030 ( 0 hom., 6 hem., cov: 22)
Exomes š: 0.000039 ( 0 hom. 20 hem. )
Consequence
PJA1
NM_001032396.4 missense
NM_001032396.4 missense
Scores
3
13
Clinical Significance
Conservation
PhyloP100: 4.16
Genes affected
PJA1 (HGNC:16648): (praja ring finger ubiquitin ligase 1) This gene encodes an enzyme that has E2-dependent E3 ubiquitin-protein ligase activity. This enzyme belongs to a class of ubiquitin ligases that include a RING finger motif, and it can interact with the E2 ubiquitin-conjugating enzyme UbcH5B. This gene is located in an area of chromosome X where several X-linked cognitive disability disorders have been associated, and it has also been found as part of a contiguous gene deletion associated with craniofrontonasal syndrome, though a direct link to any disorder has yet to be demonstrated. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.040031224).
BS2
High Hemizygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PJA1 | NM_001032396.4 | c.1000A>G | p.Ser334Gly | missense_variant | 2/2 | ENST00000374571.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PJA1 | ENST00000374571.5 | c.1000A>G | p.Ser334Gly | missense_variant | 2/2 | 1 | NM_001032396.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000298 AC: 33AN: 110654Hom.: 0 Cov.: 22 AF XY: 0.000183 AC XY: 6AN XY: 32868
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GnomAD3 exomes AF: 0.0000765 AC: 14AN: 183022Hom.: 0 AF XY: 0.0000886 AC XY: 6AN XY: 67692
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GnomAD4 exome AF: 0.0000392 AC: 43AN: 1098206Hom.: 0 Cov.: 34 AF XY: 0.0000550 AC XY: 20AN XY: 363566
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GnomAD4 genome AF: 0.000298 AC: 33AN: 110710Hom.: 0 Cov.: 22 AF XY: 0.000182 AC XY: 6AN XY: 32934
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.1165A>G (p.S389G) alteration is located in exon 2 (coding exon 1) of the PJA1 gene. This alteration results from a A to G substitution at nucleotide position 1165, causing the serine (S) at amino acid position 389 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;T;.
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;P;B;.
Vest4
MVP
MPC
0.60
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at