7-71388309-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_022479.3(GALNT17):c.497C>T(p.Ser166Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Consequence
GALNT17
NM_022479.3 missense
NM_022479.3 missense
Scores
13
3
2
Clinical Significance
Conservation
PhyloP100: 7.90
Genes affected
GALNT17 (HGNC:16347): (polypeptide N-acetylgalactosaminyltransferase 17) This gene encodes an N-acetylgalactosaminyltransferase. This gene is located centromeric to the common deleted region in Williams-Beuren syndrome (WBS), a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. This protein may play a role in membrane trafficking. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.928
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT17 | NM_022479.3 | c.497C>T | p.Ser166Leu | missense_variant | 3/11 | ENST00000333538.10 | NP_071924.1 | |
GALNT17 | XM_011516467.4 | c.497C>T | p.Ser166Leu | missense_variant | 3/10 | XP_011514769.1 | ||
GALNT17 | XM_017012521.3 | c.497C>T | p.Ser166Leu | missense_variant | 3/7 | XP_016868010.1 | ||
GALNT17 | XM_011516469.4 | c.497C>T | p.Ser166Leu | missense_variant | 3/6 | XP_011514771.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT17 | ENST00000333538.10 | c.497C>T | p.Ser166Leu | missense_variant | 3/11 | 1 | NM_022479.3 | ENSP00000329654.5 | ||
GALNT17 | ENST00000447516.5 | c.431C>T | p.Ser144Leu | missense_variant | 3/4 | 4 | ENSP00000392019.1 | |||
GALNT17 | ENST00000467723.1 | n.431C>T | non_coding_transcript_exon_variant | 3/11 | 2 | |||||
GALNT17 | ENST00000498380.6 | n.899C>T | non_coding_transcript_exon_variant | 3/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.497C>T (p.S166L) alteration is located in exon 3 (coding exon 3) of the WBSCR17 gene. This alteration results from a C to T substitution at nucleotide position 497, causing the serine (S) at amino acid position 166 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;.
REVEL
Pathogenic
Sift
Pathogenic
D;D;.
Sift4G
Pathogenic
D;D;D
Polyphen
D;.;.
Vest4
MutPred
Loss of catalytic residue at S166 (P = 0.3018);.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.