1-62017888-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001350145.3(PATJ):c.3900C>G(p.His1300Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000695 in 1,611,754 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 Uncertain significance (★).
Frequency
Consequence
NM_001350145.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PATJ | NM_001350145.3 | c.3900C>G | p.His1300Gln | missense_variant | Exon 29 of 44 | ENST00000642238.2 | NP_001337074.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PATJ | ENST00000642238.2 | c.3900C>G | p.His1300Gln | missense_variant | Exon 29 of 44 | NM_001350145.3 | ENSP00000494277.1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152048Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251194Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135750
GnomAD4 exome AF: 0.0000685 AC: 100AN: 1459588Hom.: 0 Cov.: 28 AF XY: 0.0000633 AC XY: 46AN XY: 726228
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74404
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3900C>G (p.H1300Q) alteration is located in exon 29 (coding exon 28) of the PATJ gene. This alteration results from a C to G substitution at nucleotide position 3900, causing the histidine (H) at amino acid position 1300 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at