1-156873858-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_002529.4(NTRK1):āc.1076A>Gā(p.Tyr359Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,454,308 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Y359Y) has been classified as Likely benign.
Frequency
Consequence
NM_002529.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.1076A>G | p.Tyr359Cys | missense_variant | 8/17 | ENST00000524377.7 | NP_002520.2 | |
NTRK1 | NM_001012331.2 | c.1076A>G | p.Tyr359Cys | missense_variant | 8/16 | NP_001012331.1 | ||
NTRK1 | NM_001007792.1 | c.986A>G | p.Tyr329Cys | missense_variant | 9/17 | NP_001007793.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1454308Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 722762
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Hereditary insensitivity to pain with anhidrosis Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 2002 | - - |
Charcot-Marie-Tooth disease Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Inherited Neuropathy Consortium | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at