1-230178306-C-T
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_004481.5(GALNT2):c.215C>T(p.Pro72Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,612,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004481.5 missense
Scores
Clinical Significance
Conservation
Publications
- congenital disorder of glycosylation, type iitInheritance: AR Classification: STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics
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ACMG classification
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT2 | NM_004481.5 | c.215C>T | p.Pro72Leu | missense_variant | Exon 2 of 16 | ENST00000366672.5 | NP_004472.1 | |
GALNT2 | NM_001291866.2 | c.101C>T | p.Pro34Leu | missense_variant | Exon 2 of 16 | NP_001278795.1 | ||
GALNT2 | XM_017000964.3 | c.122C>T | p.Pro41Leu | missense_variant | Exon 3 of 17 | XP_016856453.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000399 AC: 1AN: 250754 AF XY: 0.00000738 show subpopulations
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460724Hom.: 0 Cov.: 29 AF XY: 0.00000688 AC XY: 5AN XY: 726744 show subpopulations
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74354 show subpopulations
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.215C>T (p.P72L) alteration is located in exon 2 (coding exon 2) of the GALNT2 gene. This alteration results from a C to T substitution at nucleotide position 215, causing the proline (P) at amino acid position 72 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