chr1-24449609-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020448.5(NIPAL3):c.523C>T(p.Pro175Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,280 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_020448.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NIPAL3 | ENST00000374399.9 | c.523C>T | p.Pro175Ser | missense_variant | Exon 6 of 12 | 1 | NM_020448.5 | ENSP00000363520.4 | ||
NIPAL3 | ENST00000003912.7 | c.277C>T | p.Pro93Ser | missense_variant | Exon 7 of 13 | 1 | ENSP00000003912.3 | |||
NIPAL3 | ENST00000358028.8 | c.523C>T | p.Pro175Ser | missense_variant | Exon 6 of 8 | 1 | ENSP00000350722.4 | |||
NIPAL3 | ENST00000339255.2 | c.523C>T | p.Pro175Ser | missense_variant | Exon 6 of 12 | 5 | ENSP00000343549.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461280Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726898
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.523C>T (p.P175S) alteration is located in exon 6 (coding exon 5) of the NIPAL3 gene. This alteration results from a C to T substitution at nucleotide position 523, causing the proline (P) at amino acid position 175 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.