rs1555059203
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_015459.5(ATL3):c.5_7delinsCTG(p.Leu2_Ser3delinsSerAla) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
ATL3
NM_015459.5 missense
NM_015459.5 missense
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.84
Genes affected
ATL3 (HGNC:24526): (atlastin GTPase 3) This gene encodes a member of a family of dynamin-like, integral membrane GTPases. The encoded protein is required for the proper formation of the network of interconnected tubules of the endoplasmic reticulum. Mutations in this gene may be associated with hereditary sensory neuropathy type IF. Alternatively spliced transcript variants that encode distinct isoforms have been described. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATL3 | NM_015459.5 | c.5_7delinsCTG | p.Leu2_Ser3delinsSerAla | missense_variant | 1/13 | ENST00000398868.8 | |
ATL3 | XM_006718493.2 | c.5_7delinsCTG | p.Leu2_Ser3delinsSerAla | missense_variant | 1/12 | ||
ATL3 | XM_047426725.1 | c.161_163delinsCTG | p.Leu54_Ser55delinsSerAla | missense_variant | 2/14 | ||
ATL3 | NM_001290048.2 | c.-9+305_-9+307delinsCTG | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATL3 | ENST00000398868.8 | c.5_7delinsCTG | p.Leu2_Ser3delinsSerAla | missense_variant | 1/13 | 1 | NM_015459.5 | ||
ATL3 | ENST00000540699.1 | c.161_163delinsCTG | p.Leu54_Ser55delinsSerAla | missense_variant | 2/4 | 3 | |||
ATL3 | ENST00000538786.1 | c.-9+305_-9+307delinsCTG | intron_variant | 2 | P1 | ||||
ATL3 | ENST00000535789.1 | n.416_418delinsCTG | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neuropathy, hereditary sensory, type 1F Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 29, 2023 | This variant, c.5_7delinsCTG, is a complex sequence change that results in the deletion of 2 and insertion of 2 amino acid(s) in the ATL3 protein (p.Leu2_Ser3delinsSerAla). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with ATL3-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at