NM_020975.6:c.2719A>T
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PM2
The NM_020975.6(RET):c.2719A>T(p.Lys907*) variant causes a stop gained 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. K907K) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_020975.6 stop_gained
Scores
Clinical Significance
Conservation
Publications
- familial medullary thyroid carcinomaInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P
- multiple endocrine neoplasia type 2AInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen, G2P
- multiple endocrine neoplasia type 2BInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen
- pheochromocytomaInheritance: AD Classification: DEFINITIVE Submitted by: G2P
- Hirschsprung disease, susceptibility to, 1Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Haddad syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Hirschsprung diseaseInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- renal agenesis, unilateralInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- bilateral renal agenesisInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- renal agenesisInheritance: AR Classification: LIMITED Submitted by: G2P
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ACMG classification
Our verdict: Pathogenic. The variant received 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RET | NM_020975.6 | c.2719A>T | p.Lys907* | stop_gained | Exon 15 of 20 | ENST00000355710.8 | NP_066124.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at