rs121913671
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_000245.4(MET):c.3682G>A(p.Asp1228Asn) 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1228H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000245.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MET | NM_000245.4 | c.3682G>A | p.Asp1228Asn | missense_variant | 19/21 | ENST00000397752.8 | |
MET | NM_001127500.3 | c.3736G>A | p.Asp1246Asn | missense_variant | 19/21 | ||
MET | NM_001324402.2 | c.2392G>A | p.Asp798Asn | missense_variant | 18/20 | ||
MET | XM_011516223.2 | c.3739G>A | p.Asp1247Asn | missense_variant | 20/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MET | ENST00000397752.8 | c.3682G>A | p.Asp1228Asn | missense_variant | 19/21 | 1 | NM_000245.4 | P3 | |
MET | ENST00000318493.11 | c.3736G>A | p.Asp1246Asn | missense_variant | 19/21 | 1 | A2 | ||
MET | ENST00000436117.3 | c.*1287G>A | 3_prime_UTR_variant, NMD_transcript_variant | 18/20 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Carcinoma Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Database of Curated Mutations (DoCM) | May 13, 2016 | - - |
Papillary renal cell carcinoma type 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at