3-141293078-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001037172.3(PXYLP1):c.1316A>T(p.His439Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H439Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001037172.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PXYLP1 | NM_001037172.3 | c.1316A>T | p.His439Leu | missense_variant | 6/6 | ENST00000286353.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXYLP1 | ENST00000286353.9 | c.1316A>T | p.His439Leu | missense_variant | 6/6 | 1 | NM_001037172.3 | P1 | |
ENST00000507698.1 | n.167-25470T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251150Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135738
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727248
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2023 | The c.1316A>T (p.H439L) alteration is located in exon 8 (coding exon 5) of the PXYLP1 gene. This alteration results from a A to T substitution at nucleotide position 1316, causing the histidine (H) at amino acid position 439 to be replaced by a leucine (L). 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