NM_006762.3:c.458G>C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006762.3(LAPTM5):c.458G>C(p.Ser153Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000000687 in 1,455,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006762.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAPTM5 | NM_006762.3 | c.458G>C | p.Ser153Thr | missense_variant | Exon 5 of 8 | ENST00000294507.4 | NP_006753.1 | |
LAPTM5 | XM_011542098.3 | c.287G>C | p.Ser96Thr | missense_variant | Exon 3 of 6 | XP_011540400.1 | ||
MIR4420 | NR_039616.1 | n.*164G>C | downstream_gene_variant | |||||
MIR4420 | unassigned_transcript_62 | n.*166G>C | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAPTM5 | ENST00000294507.4 | c.458G>C | p.Ser153Thr | missense_variant | Exon 5 of 8 | 1 | NM_006762.3 | ENSP00000294507.3 | ||
LAPTM5 | ENST00000464569.1 | n.683G>C | non_coding_transcript_exon_variant | Exon 5 of 8 | 5 | |||||
MIR4420 | ENST00000583944.1 | n.*164G>C | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455936Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 723634
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.458G>C (p.S153T) alteration is located in exon 5 (coding exon 5) of the LAPTM5 gene. This alteration results from a G to C substitution at nucleotide position 458, causing the serine (S) at amino acid position 153 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at