12-63805410-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_014254.3(RXYLT1):c.914+6T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000699 in 1,574,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014254.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXYLT1 | NM_014254.3 | c.914+6T>G | splice_region_variant, intron_variant | Intron 5 of 5 | ENST00000261234.11 | NP_055069.1 | ||
RXYLT1 | NM_001278237.2 | c.134+6T>G | splice_region_variant, intron_variant | Intron 5 of 5 | NP_001265166.1 | |||
RXYLT1 | XM_047428078.1 | c.605+6T>G | splice_region_variant, intron_variant | Intron 4 of 4 | XP_047284034.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000916 AC: 2AN: 218386Hom.: 0 AF XY: 0.0000169 AC XY: 2AN XY: 118326
GnomAD4 exome AF: 0.00000633 AC: 9AN: 1422032Hom.: 0 Cov.: 30 AF XY: 0.00000567 AC XY: 4AN XY: 705662
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:1
This sequence change falls in intron 5 of the RXYLT1 gene. It does not directly change the encoded amino acid sequence of the RXYLT1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs748809209, gnomAD 0.002%). This variant has been observed in individual(s) with clinical features of congenital muscular dystrophy (PMID: 30017359). ClinVar contains an entry for this variant (Variation ID: 429848). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 5, but is expected to preserve the integrity of the reading-frame (PMID: 30017359). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
A variant of uncertain significance has been identified in the TMEM5 gene. The c.914+6 T>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.914+6 T>G variant not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Several in-silico splice prediction models predict that c.914+6 T>G reduces the natural splice donor site and may and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant. -
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 Pathogenic:1Uncertain:1
- -
Variant summary: RXYLT1 c.914+6T>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant weakens a 5' donor site. One predicts the variant creates a 5' donor site. One predicts the variant no significant impact on splicing. At least one publication reports experimental evidence that this variant affects mRNA splicing result in an in frame skipping of exon 5 in patient samples (example, Zaum_2018). The variant allele was found at a frequency of 7e-06 in 1574158 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in RXYLT1 causing Muscular Dystrophy-Dystroglycanopathy (congenital With Brain And Eye Anomalies), Type A, 10. c.914+6T>G has been reported in the homozygous state in the literature in multiple individuals affected with clinical features of Muscular Dystrophy-Dystroglycanopathy (congenital With Brain And Eye Anomalies), Type A, 10 (example, Al-Kasbi_2022, Zaum_2018), including at least 1 family where it segregated with disease. These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 36344539, 30017359). ClinVar contains an entry for this variant (Variation ID: 429848). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Inborn genetic diseases Uncertain:1
The c.914+6T>G intronic alteration consists of a T to G substitution nucleotides after coding exon 5 in the TMEM5 gene. 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