12-9149576-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002864.3(PZP):c.4411G>A(p.Ala1471Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,611,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002864.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PZP | NM_002864.3 | c.4411G>A | p.Ala1471Thr | missense_variant | Exon 35 of 36 | ENST00000261336.7 | NP_002855.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PZP | ENST00000261336.7 | c.4411G>A | p.Ala1471Thr | missense_variant | Exon 35 of 36 | 1 | NM_002864.3 | ENSP00000261336.2 | ||
PZP | ENST00000535230.5 | n.*3880G>A | non_coding_transcript_exon_variant | Exon 32 of 33 | 1 | ENSP00000440811.1 | ||||
PZP | ENST00000535230.5 | n.*3880G>A | 3_prime_UTR_variant | Exon 32 of 33 | 1 | ENSP00000440811.1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151638Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250834Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135560
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1459840Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 726238
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151638Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73996
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4411G>A (p.A1471T) alteration is located in exon 35 (coding exon 35) of the PZP gene. This alteration results from a G to A substitution at nucleotide position 4411, causing the alanine (A) at amino acid position 1471 to be replaced by a threonine (T). 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