NM_006307.5:c.1166G>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_006307.5(SRPX):c.1166G>T(p.Arg389Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000747 in 1,205,321 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006307.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX | ENST00000378533.4 | c.1166G>T | p.Arg389Met | missense_variant | Exon 9 of 10 | 1 | NM_006307.5 | ENSP00000367794.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-511614C>A | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 111949Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34107
GnomAD3 exomes AF: 0.00000584 AC: 1AN: 171266Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 57152
GnomAD4 exome AF: 0.00000732 AC: 8AN: 1093372Hom.: 0 Cov.: 30 AF XY: 0.00000278 AC XY: 1AN XY: 359384
GnomAD4 genome AF: 0.00000893 AC: 1AN: 111949Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34107
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1166G>T (p.R389M) alteration is located in exon 9 (coding exon 9) of the SRPX gene. This alteration results from a G to T substitution at nucleotide position 1166, causing the arginine (R) at amino acid position 389 to be replaced by a methionine (M). 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