6-116666717-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001361190.2(ZUP1):c.-29G>A variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00000124 in 1,613,336 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_001361190.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZUP1 | NM_145062.3 | c.476G>A | p.Cys159Tyr | missense_variant | Exon 2 of 10 | ENST00000368576.8 | NP_659499.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZUP1 | ENST00000368576.8 | c.476G>A | p.Cys159Tyr | missense_variant | Exon 2 of 10 | 1 | NM_145062.3 | ENSP00000357565.3 | ||
ZUP1 | ENST00000368573.5 | c.476G>A | p.Cys159Tyr | missense_variant | Exon 2 of 5 | 5 | ENSP00000357562.1 | |||
ZUP1 | ENST00000471919.1 | n.425G>A | non_coding_transcript_exon_variant | Exon 2 of 7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461116Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726806
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.476G>A (p.C159Y) alteration is located in exon 2 (coding exon 1) of the ZUFSP gene. This alteration results from a G to A substitution at nucleotide position 476, causing the cysteine (C) at amino acid position 159 to be replaced by a tyrosine (Y). 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