6-44254779-ACT-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_178148.4(SLC35B2):c.1224_1225del(p.Arg408SerfsTer18) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000514 in 1,613,638 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
SLC35B2
NM_178148.4 frameshift
NM_178148.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.74
Genes affected
SLC35B2 (HGNC:16872): (solute carrier family 35 member B2) Sulfotransferases (e.g., SULT4A1; MIM 608359) use an activated form of sulfate, 3-prime-phosphoadenosine 5-prime-phosphosulfate (PAPS), as a common sulfate donor for sulfation of glycoproteins, proteoglycans, and glycolipids in the endoplasmic reticulum and Golgi apparatus. SLC35B2 is located in the microsomal membrane and transports PAPS from the cytosol, where it is synthesized, into the Golgi lumen (Kamiyama et al., 2003 [PubMed 12716889]).[supplied by OMIM, Mar 2008]
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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;
PP5
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Variant 6-44254779-ACT-A is Pathogenic according to our data. Variant chr6-44254779-ACT-A is described in ClinVar as [Pathogenic]. Clinvar id is 2443960.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35B2 | NM_178148.4 | c.1224_1225del | p.Arg408SerfsTer18 | frameshift_variant | 4/4 | ENST00000393812.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35B2 | ENST00000393812.4 | c.1224_1225del | p.Arg408SerfsTer18 | frameshift_variant | 4/4 | 1 | NM_178148.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151748Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251394Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135866
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GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461890Hom.: 0 AF XY: 0.0000468 AC XY: 34AN XY: 727246
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leukodystrophy, hypomyelinating, 26, with chondrodysplasia Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 28, 2023 | - - |
Pathogenic, criteria provided, single submitter | research | Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL) | Apr 27, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at