NM_024663.4:c.258C>G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024663.4(NPEPL1):c.258C>G(p.His86Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000496 in 1,613,546 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024663.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPEPL1 | NM_024663.4 | c.258C>G | p.His86Gln | missense_variant | Exon 2 of 12 | ENST00000356091.11 | NP_078939.3 | |
NPEPL1 | NM_001204872.2 | c.174C>G | p.His58Gln | missense_variant | Exon 3 of 13 | NP_001191801.1 | ||
NPEPL1 | NM_001204873.2 | c.114C>G | p.His38Gln | missense_variant | Exon 3 of 13 | NP_001191802.1 | ||
STX16-NPEPL1 | NR_037945.1 | n.2144C>G | non_coding_transcript_exon_variant | Exon 12 of 23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPEPL1 | ENST00000356091.11 | c.258C>G | p.His86Gln | missense_variant | Exon 2 of 12 | 1 | NM_024663.4 | ENSP00000348395.6 | ||
STX16-NPEPL1 | ENST00000530122.1 | n.*241C>G | non_coding_transcript_exon_variant | Exon 12 of 23 | 5 | ENSP00000457522.1 | ||||
STX16-NPEPL1 | ENST00000530122.1 | n.*241C>G | 3_prime_UTR_variant | Exon 12 of 23 | 5 | ENSP00000457522.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152242Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247066Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134480
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461304Hom.: 0 Cov.: 37 AF XY: 0.00000275 AC XY: 2AN XY: 726972
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152242Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.258C>G (p.H86Q) alteration is located in exon 2 (coding exon 2) of the NPEPL1 gene. This alteration results from a C to G substitution at nucleotide position 258, causing the histidine (H) at amino acid position 86 to be replaced by a glutamine (Q). 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