rs775516790
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001384125.1(BLTP1):โc.3611delโ(p.Asn1204ThrfsTer6) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000124 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: ๐ 0.0000066 ( 0 hom., cov: 32)
Exomes ๐: 6.8e-7 ( 0 hom. )
Consequence
BLTP1
NM_001384125.1 frameshift
NM_001384125.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.73
Genes affected
BLTP1 (HGNC:26953): (bridge-like lipid transfer protein family member 1) This gene is located on the long arm of chromosome 4 in a region that is associated with susceptibility to celiac disease. The encoded protein is similar to a Chinese hamster protein that is associated with spermatocyte and adipocyte differentiation. The C-terminus of the protein is also similar to a Caenorhabditis elegans protein that plays a role in lipid storage. In mammals, this protein is thought to function in the regulation of epithelial growth and differentiation, and in tumor development. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 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 4-122238124-GA-G is Pathogenic according to our data. Variant chr4-122238124-GA-G is described in ClinVar as [Pathogenic]. Clinvar id is 487549.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr4-122238124-GA-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLTP1 | NM_001384125.1 | c.3611del | p.Asn1204ThrfsTer6 | frameshift_variant | 28/88 | ENST00000679879.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLTP1 | ENST00000679879.1 | c.3611del | p.Asn1204ThrfsTer6 | frameshift_variant | 28/88 | NM_001384125.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249302Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135248
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461716Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727172
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74310
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Alkuraya-Kucinskas syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 11, 2018 | - - |
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