NM_001543.5:c.179C>T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001543.5(NDST1):c.179C>T(p.Pro60Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,612,978 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001543.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDST1 | ENST00000261797.7 | c.179C>T | p.Pro60Leu | missense_variant | Exon 2 of 15 | 1 | NM_001543.5 | ENSP00000261797.6 | ||
NDST1 | ENST00000523767.5 | c.179C>T | p.Pro60Leu | missense_variant | Exon 2 of 14 | 2 | ENSP00000428604.1 | |||
NDST1 | ENST00000519157.1 | c.179C>T | p.Pro60Leu | missense_variant | Exon 2 of 2 | 5 | ENSP00000427813.1 | |||
NDST1 | ENST00000522491.1 | c.179C>T | p.Pro60Leu | missense_variant | Exon 2 of 2 | 2 | ENSP00000429966.1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000566 AC: 14AN: 247418Hom.: 0 AF XY: 0.0000745 AC XY: 10AN XY: 134244
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1460774Hom.: 1 Cov.: 31 AF XY: 0.0000372 AC XY: 27AN XY: 726746
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.179C>T (p.P60L) alteration is located in exon 2 (coding exon 1) of the NDST1 gene. This alteration results from a C to T substitution at nucleotide position 179, causing the proline (P) at amino acid position 60 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