8-16110212-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_138715.3(MSR1):c.1229G>T(p.Gly410Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,180 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 (★).
Frequency
Consequence
NM_138715.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSR1 | NM_138715.3 | c.1229G>T | p.Gly410Val | missense_variant | Exon 10 of 10 | ENST00000262101.10 | NP_619729.1 | |
MSR1 | NM_001363744.1 | c.1283G>T | p.Gly428Val | missense_variant | Exon 10 of 10 | NP_001350673.1 | ||
MSR1 | NM_138716.3 | c.1040G>T | p.Gly347Val | missense_variant | Exon 9 of 9 | NP_619730.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSR1 | ENST00000262101.10 | c.1229G>T | p.Gly410Val | missense_variant | Exon 10 of 10 | 1 | NM_138715.3 | ENSP00000262101.5 | ||
MSR1 | ENST00000445506.6 | c.1283G>T | p.Gly428Val | missense_variant | Exon 10 of 10 | 1 | ENSP00000405453.2 | |||
MSR1 | ENST00000355282.6 | c.1040G>T | p.Gly347Val | missense_variant | Exon 8 of 8 | 1 | ENSP00000347430.2 | |||
MSR1 | ENST00000350896.3 | c.1040G>T | p.Gly347Val | missense_variant | Exon 9 of 9 | 5 | ENSP00000262100.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461180Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726892
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1229G>T (p.G410V) alteration is located in exon 10 (coding exon 9) of the MSR1 gene. This alteration results from a G to T substitution at nucleotide position 1229, causing the glycine (G) at amino acid position 410 to be replaced by a valine (V). 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