rs121912681
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PM4_SupportingPP5_Very_Strong
The NM_000485.3(APRT):c.521_523delTCT(p.Phe174del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000632 in 1,613,428 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_000485.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152232Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250756Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135748
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461078Hom.: 0 AF XY: 0.0000578 AC XY: 42AN XY: 726832
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152350Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74500
ClinVar
Submissions by phenotype
Adenine phosphoribosyltransferase deficiency Pathogenic:3Uncertain:1
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See cases Pathogenic:1
ACMG classification criteria: PS3, PM2, PM3, PM4 -
not provided Pathogenic:1
This variant is also known as c.517_519delTTC. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 18294). This variant has been observed in individual(s) with adenine phosphoribosyltransferase deficiency (PMID: 3680503, 23430916). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs751152783, gnomAD 0.03%). This variant, c.521_523del, results in the deletion of 1 amino acid(s) of the APRT protein (p.Phe174del), but otherwise preserves the integrity of the reading frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at