chrX-24562316-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004845.5(PCYT1B):c.1087G>A(p.Glu363Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000668 in 1,047,957 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004845.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCYT1B | NM_004845.5 | c.1087G>A | p.Glu363Lys | missense_variant | Exon 8 of 8 | ENST00000379144.7 | NP_004836.2 | |
PCYT1B | NM_001163264.2 | c.1033G>A | p.Glu345Lys | missense_variant | Exon 8 of 8 | NP_001156736.1 | ||
PCYT1B | XM_017029977.2 | c.799G>A | p.Glu267Lys | missense_variant | Exon 9 of 9 | XP_016885466.1 | ||
PCYT1B | NM_001163265.2 | c.960+127G>A | intron_variant | Intron 8 of 8 | NP_001156737.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCYT1B | ENST00000379144.7 | c.1087G>A | p.Glu363Lys | missense_variant | Exon 8 of 8 | 1 | NM_004845.5 | ENSP00000368439.2 | ||
PCYT1B | ENST00000379145.5 | c.1033G>A | p.Glu345Lys | missense_variant | Exon 8 of 8 | 1 | ENSP00000368440.1 | |||
PCYT1B | ENST00000356768.8 | c.960+127G>A | intron_variant | Intron 8 of 8 | 1 | ENSP00000349211.4 | ||||
PCYT1B | ENST00000496020.1 | n.*396G>A | downstream_gene_variant | 3 | ENSP00000436562.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000668 AC: 7AN: 1047957Hom.: 0 Cov.: 30 AF XY: 0.00000898 AC XY: 3AN XY: 333939
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1087G>A (p.E363K) alteration is located in exon 8 (coding exon 8) of the PCYT1B gene. This alteration results from a G to A substitution at nucleotide position 1087, causing the glutamic acid (E) at amino acid position 363 to be replaced by a lysine (K). 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