NM_001189.4:c.898C>G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001189.4(NKX3-2):āc.898C>Gā(p.Arg300Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,252 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001189.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NKX3-2 | NM_001189.4 | c.898C>G | p.Arg300Gly | missense_variant | Exon 2 of 2 | ENST00000382438.6 | NP_001180.1 | |
NKX3-2 | XM_047416049.1 | c.898C>G | p.Arg300Gly | missense_variant | Exon 3 of 3 | XP_047272005.1 | ||
NKX3-2 | XM_047416050.1 | c.898C>G | p.Arg300Gly | missense_variant | Exon 3 of 3 | XP_047272006.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.898C>G (p.R300G) alteration is located in exon 2 (coding exon 2) of the NKX3-2 gene. This alteration results from a C to G substitution at nucleotide position 898, causing the arginine (R) at amino acid position 300 to be replaced by a glycine (G). 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