rs111033638
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000155.4(GALT):βc.18delβ(p.Asp7IlefsTer43) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,446 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (β β ). Synonymous variant affecting the same amino acid position (i.e. T6T) has been classified as Likely benign.
Frequency
Consequence
NM_000155.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALT | NM_000155.4 | c.18del | p.Asp7IlefsTer43 | frameshift_variant | 1/11 | ENST00000378842.8 | |
GALT | NM_001258332.2 | c.-185del | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALT | ENST00000378842.8 | c.18del | p.Asp7IlefsTer43 | frameshift_variant | 1/11 | 1 | NM_000155.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461446Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727038
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 24, 2023 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Mar 07, 2016 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 20, 2022 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 25113). This variant is also known as T6fsdelC. This premature translational stop signal has been observed in individual(s) with clinical features of galactose-1-phosphate uridylyltransferase deficiency (PMID: 15775761). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asp7Ilefs*43) in the GALT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GALT are known to be pathogenic (PMID: 22944367). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at