rs587777378
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PM4_SupportingPP5_Very_Strong
The NM_024989.4(PGAP1):c.589_591delCTT(p.Leu197del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,762 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_024989.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251040Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135672
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461570Hom.: 0 AF XY: 0.00000963 AC XY: 7AN XY: 727080
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
Intellectual disability, autosomal recessive 42 Pathogenic:3
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Review of the variants reported in Reuter et al., 2017, PMID: 28097321: PS3,PM2,PM3_Supporting -
The inframe deletion variant c.589_591del(p.Leu197del) in PGAP1 gene has been reported in affected individuals in the literature (Murakami Y et.al.,2014). This variant has been reported to the ClinVar database as Pathogenic/Likely Pathogenic. The p.Leu197del variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.0007081% is reported in gnomAD. This p.Leu197del causes deletion of amino acid Leucine at position 197. For these reasons, this variant has been classified as Pathogenic . -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at