X-101397801-TAAACATTTTAAA-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_000169.3(GLA):c.1286_*7delTTTAAAATGTTT(p.Leu429fs) variant causes a frameshift, stop lost, 3 prime UTR truncation, exon loss, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 23)
Consequence
GLA
NM_000169.3 frameshift, stop_lost, 3_prime_UTR_truncation, exon_loss, splice_region
NM_000169.3 frameshift, stop_lost, 3_prime_UTR_truncation, exon_loss, splice_region
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
GLA (HGNC:4296): (galactosidase alpha) This gene encodes a homodimeric glycoprotein that hydrolyses the terminal alpha-galactosyl moieties from glycolipids and glycoproteins. This enzyme predominantly hydrolyzes ceramide trihexoside, and it can catalyze the hydrolysis of melibiose into galactose and glucose. A variety of mutations in this gene affect the synthesis, processing, and stability of this enzyme, which causes Fabry disease, a rare lysosomal storage disorder that results from a failure to catabolize alpha-D-galactosyl glycolipid moieties. [provided by RefSeq, Jul 2008]
RPL36A-HNRNPH2 (HGNC:48349): (RPL36A-HNRNPH2 readthrough) This locus represents naturally occurring read-through transcription between the neighboring ribosomal protein L36a and heterogeneous nuclear ribonucleoprotein H2 (H') genes on chromosome X. The read-through transcript produces a protein with similarity to the protein encoded by the upstream locus, ribosomal protein L36a. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Jan 2011]
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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;
PM4
Stoplost variant in NM_000169.3
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLA | NM_000169.3 | c.1286_*7delTTTAAAATGTTT | p.Leu429fs | frameshift_variant, stop_lost, 3_prime_UTR_truncation, exon_loss_variant, splice_region_variant | 7/7 | ENST00000218516.4 | NP_000160.1 | |
GLA | NM_000169.3 | c.1286_*7delTTTAAAATGTTT | downstream_gene_variant | ENST00000218516.4 | NP_000160.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLA | ENST00000218516.4 | c.1286_*7delTTTAAAATGTTT | p.Leu429fs | frameshift_variant, stop_lost, 3_prime_UTR_truncation, exon_loss_variant, splice_region_variant | 7/7 | 1 | NM_000169.3 | ENSP00000218516.4 | ||
RPL36A-HNRNPH2 | ENST00000409170.3 | c.300+2345_300+2356delAAACATTTTAAA | intron_variant | 4 | ENSP00000386655.4 | |||||
GLA | ENST00000218516.4 | c.1286_*7delTTTAAAATGTTT | downstream_gene_variant | 1 | NM_000169.3 | ENSP00000218516.4 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
Cov.:
23
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 23
GnomAD4 genome
Cov.:
23
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 29, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.