1-1232684-GTGCTGGCCA-G
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Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_080605.4(B3GALT6):c.415_423del(p.Met139_Ala141del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000215 in 1,394,302 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Consequence
B3GALT6
NM_080605.4 inframe_deletion
NM_080605.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.84
Genes affected
B3GALT6 (HGNC:17978): (beta-1,3-galactosyltransferase 6) The enzyme encoded by this intronless gene is a beta-1,3-galactosyltransferase found in the medial Golgi apparatus, where it catalyzes the transfer of galactose from UDP-galactose to substrates containing a terminal beta-linked galactose moiety. The encoded enzyme has a particular affinity for galactose-beta-1,4-xylose found in the linker region of glycosamines. This enzyme is required for glycosaminoglycan synthesis. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_080605.4.
PP5
Variant 1-1232684-GTGCTGGCCA-G is Pathogenic according to our data. Variant chr1-1232684-GTGCTGGCCA-G is described in ClinVar as [Pathogenic]. Clinvar id is 60494.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| B3GALT6 | NM_080605.4 | c.415_423del | p.Met139_Ala141del | inframe_deletion | 1/1 | ENST00000379198.5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| B3GALT6 | ENST00000379198.5 | c.415_423del | p.Met139_Ala141del | inframe_deletion | 1/1 | NM_080605.4 | P1 |
Frequencies
GnomAD3 genomes 0.00000663 AC: 1AN: 150724Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000161 AC: 2AN: 1243578Hom.: 0 AF XY: 0.00000326 AC XY: 2AN XY: 612714
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GnomAD4 genome 0.00000663 AC: 1AN: 150724Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 73562
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Ehlers-Danlos syndrome, spondylodysplastic type, 2 Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 06, 2013 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at