rs556318081
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PM5BP4_Moderate
The NM_024312.5(GNPTAB):āc.3707A>Gā(p.Lys1236Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000459 in 1,569,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K1236M) has been classified as Likely pathogenic.
Frequency
Consequence
NM_024312.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPTAB | NM_024312.5 | c.3707A>G | p.Lys1236Arg | missense_variant | 21/21 | ENST00000299314.12 | |
GNPTAB | XM_011538731.3 | c.3626A>G | p.Lys1209Arg | missense_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.3707A>G | p.Lys1236Arg | missense_variant | 21/21 | 1 | NM_024312.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251088Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135734
GnomAD4 exome AF: 0.0000480 AC: 68AN: 1416876Hom.: 0 Cov.: 24 AF XY: 0.0000607 AC XY: 43AN XY: 707854
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74506
ClinVar
Submissions by phenotype
Pseudo-Hurler polydystrophy;C2673377:Mucolipidosis type II Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Oct 03, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at