chr16-17108768-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_022166.4(XYLT1):c.2807C>T(p.Thr936Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000677 in 1,608,864 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T936S) has been classified as Uncertain significance.
Frequency
Consequence
NM_022166.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XYLT1 | NM_022166.4 | c.2807C>T | p.Thr936Met | missense_variant | 12/12 | ENST00000261381.7 | |
XYLT1 | XM_047434458.1 | c.2768C>T | p.Thr923Met | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XYLT1 | ENST00000261381.7 | c.2807C>T | p.Thr936Met | missense_variant | 12/12 | 1 | NM_022166.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000607 AC: 15AN: 246942Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 133926
GnomAD4 exome AF: 0.0000700 AC: 102AN: 1456526Hom.: 0 Cov.: 30 AF XY: 0.0000842 AC XY: 61AN XY: 724640
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74492
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital | Jan 06, 2020 | - - |
Desbuquois dysplasia 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 936 of the XYLT1 protein (p.Thr936Met). This variant is present in population databases (rs768752782, gnomAD 0.05%). This missense change has been observed in individual(s) with nonsyndromic early onset high myopia (PMID: 28085539). ClinVar contains an entry for this variant (Variation ID: 1301770). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on XYLT1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at