7-7238549-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_020156.5(C1GALT1):c.515C>T(p.Thr172Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020156.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1GALT1 | NM_020156.5 | c.515C>T | p.Thr172Met | missense_variant | Exon 3 of 4 | ENST00000436587.7 | NP_064541.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1GALT1 | ENST00000436587.7 | c.515C>T | p.Thr172Met | missense_variant | Exon 3 of 4 | 5 | NM_020156.5 | ENSP00000389176.2 | ||
C1GALT1 | ENST00000223122.4 | c.515C>T | p.Thr172Met | missense_variant | Exon 2 of 3 | 1 | ENSP00000223122.2 | |||
C1GALT1 | ENST00000402468.3 | c.515C>T | p.Thr172Met | missense_variant | Exon 2 of 2 | 1 | ENSP00000384550.3 | |||
C1GALT1 | ENST00000429911.5 | c.*121C>T | downstream_gene_variant | 5 | ENSP00000407666.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250882Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135804
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461762Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727188
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.515C>T (p.T172M) alteration is located in exon 3 (coding exon 2) of the C1GALT1 gene. This alteration results from a C to T substitution at nucleotide position 515, causing the threonine (T) at amino acid position 172 to be replaced by a methionine (M). 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