rs386833501
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_000112.4(SLC26A2):c.2120_2121delTT(p.Leu707fs) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
SLC26A2
NM_000112.4 frameshift
NM_000112.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.50
Genes affected
SLC26A2 (HGNC:10994): (solute carrier family 26 member 2) The diastrophic dysplasia sulfate transporter is a transmembrane glycoprotein implicated in the pathogenesis of several human chondrodysplasias. It apparently is critical in cartilage for sulfation of proteoglycans and matrix organization. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.045 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 5-149981712-CTT-C is Pathogenic according to our data. Variant chr5-149981712-CTT-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 56020.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-149981712-CTT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC26A2 | NM_000112.4 | c.2120_2121delTT | p.Leu707fs | frameshift_variant | 3/3 | ENST00000286298.5 | NP_000103.2 | |
SLC26A2 | XM_017009191.3 | c.2120_2121delTT | p.Leu707fs | frameshift_variant | 3/4 | XP_016864680.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC26A2 | ENST00000286298.5 | c.2120_2121delTT | p.Leu707fs | frameshift_variant | 3/3 | 1 | NM_000112.4 | ENSP00000286298.4 | ||
SLC26A2 | ENST00000503336.1 | c.372+3362_372+3363delTT | intron_variant | 3 | ENSP00000426053.1 |
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: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Diastrophic dysplasia Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at