chr14-36517757-G-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_001079668.3(NKX2-1):c.727C>A(p.Arg243Ser) 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. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R243C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001079668.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKX2-1 | NM_001079668.3 | c.727C>A | p.Arg243Ser | missense_variant | 3/3 | ENST00000354822.7 | |
SFTA3 | NR_161364.1 | n.89+1711C>A | intron_variant, non_coding_transcript_variant | ||||
NKX2-1 | NM_003317.4 | c.637C>A | p.Arg213Ser | missense_variant | 2/2 | ||
SFTA3 | NR_161365.1 | n.89+1711C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX2-1 | ENST00000354822.7 | c.727C>A | p.Arg243Ser | missense_variant | 3/3 | 1 | NM_001079668.3 | P4 | |
ENST00000634305.1 | n.322+68920G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1459764Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726096
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Benign hereditary chorea Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 15, 2002 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at