NM_024312.5:c.3539C>T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_024312.5(GNPTAB):c.3539C>T(p.Ser1180Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. S1180S) has been classified as Likely benign.
Frequency
Consequence
NM_024312.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.3539C>T | p.Ser1180Phe | missense_variant | Exon 19 of 21 | 1 | NM_024312.5 | ENSP00000299314.7 | ||
GNPTAB | ENST00000549738.5 | n.*146C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 4 | ENSP00000450161.1 | ||||
GNPTAB | ENST00000549738.5 | n.*146C>T | 3_prime_UTR_variant | Exon 4 of 5 | 4 | ENSP00000450161.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Pseudo-Hurler polydystrophy;C2673377:Mucolipidosis type II Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at