19-828287-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001700.5(AZU1):c.116C>T(p.Pro39Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,611,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001700.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AZU1 | ENST00000233997.4 | c.116C>T | p.Pro39Leu | missense_variant | Exon 2 of 5 | 1 | NM_001700.5 | ENSP00000233997.1 | ||
AZU1 | ENST00000592205 | c.-71C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 4 | 2 | ENSP00000481172.1 | ||||
AZU1 | ENST00000592205 | c.-71C>T | 5_prime_UTR_variant | Exon 2 of 4 | 2 | ENSP00000481172.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247788Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134718
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459438Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 725984
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.116C>T (p.P39L) alteration is located in exon 2 (coding exon 2) of the AZU1 gene. This alteration results from a C to T substitution at nucleotide position 116, causing the proline (P) at amino acid position 39 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