1-160419539-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020335.3(VANGL2):c.730C>T(p.Pro244Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000069 in 1,448,678 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020335.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL2 | ENST00000368061.3 | c.730C>T | p.Pro244Ser | missense_variant | Exon 4 of 8 | 2 | NM_020335.3 | ENSP00000357040.2 | ||
VANGL2 | ENST00000696602.1 | c.874C>T | p.Pro292Ser | missense_variant | Exon 4 of 8 | ENSP00000512747.1 | ||||
VANGL2 | ENST00000483408.1 | n.47C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448678Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 721116
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.730C>T (p.P244S) alteration is located in exon 4 (coding exon 3) of the VANGL2 gene. This alteration results from a C to T substitution at nucleotide position 730, causing the proline (P) at amino acid position 244 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.