rs786200881
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000112.4(SLC26A2):c.391del(p.Leu131CysfsTer41) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. S130S) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
SLC26A2
NM_000112.4 frameshift
NM_000112.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.08
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 Pathogenic. Variant got 18 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 5-149978040-TC-T is Pathogenic according to our data. Variant chr5-149978040-TC-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 4088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-149978040-TC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A2 | NM_000112.4 | c.391del | p.Leu131CysfsTer41 | frameshift_variant | 2/3 | ENST00000286298.5 | |
SLC26A2 | XM_017009191.3 | c.391del | p.Leu131CysfsTer41 | frameshift_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A2 | ENST00000286298.5 | c.391del | p.Leu131CysfsTer41 | frameshift_variant | 2/3 | 1 | NM_000112.4 | P1 | |
SLC26A2 | ENST00000503336.1 | c.64del | p.Leu22CysfsTer41 | frameshift_variant | 1/2 | 3 | |||
SLC26A2 | ENST00000690410.1 | n.623del | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Bravo
AF:
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Atelosteogenesis type II Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 1996 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jun 24, 2016 | - - |
Multiple epiphyseal dysplasia type 4 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jun 24, 2016 | - - |
Achondrogenesis, type IB Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jun 24, 2016 | - - |
Diastrophic dysplasia;C0265274:Achondrogenesis, type IB;C1847593:Multiple epiphyseal dysplasia type 4;C1850554:Atelosteogenesis type II Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Sep 21, 2023 | This premature translational stop signal has been observed in individual(s) with atelosteogenesis type 2 (PMID: 8931695). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 4088). This variant is also known as delta-c418. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu131Cysfs*41) in the SLC26A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC26A2 are known to be pathogenic (PMID: 7923357, 10482955, 11241838). - |
Diastrophic dysplasia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jun 24, 2016 | - - |
Computational scores
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at