rs141292909
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_014467.3(SRPX2):āc.1199A>Gā(p.Asn400Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000196 in 1,020,097 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014467.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRPX2 | NM_014467.3 | c.1199A>G | p.Asn400Ser | missense_variant | 10/11 | ENST00000373004.5 | NP_055282.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX2 | ENST00000373004.5 | c.1199A>G | p.Asn400Ser | missense_variant | 10/11 | 1 | NM_014467.3 | ENSP00000362095 | P1 | |
SRPX2 | ENST00000640282.1 | c.142-1456A>G | intron_variant | 5 | ENSP00000491188 | |||||
SRPX2 | ENST00000638920.1 | n.1202A>G | non_coding_transcript_exon_variant | 9/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000884 AC: 8AN: 90512Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 20302
GnomAD3 exomes AF: 0.0000234 AC: 4AN: 170754Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 56556
GnomAD4 exome AF: 0.0000129 AC: 12AN: 929585Hom.: 0 Cov.: 31 AF XY: 0.0000132 AC XY: 4AN XY: 303159
GnomAD4 genome AF: 0.0000884 AC: 8AN: 90512Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 20302
ClinVar
Submissions by phenotype
Rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 22, 2022 | Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 207384). This variant has not been reported in the literature in individuals affected with SRPX2-related conditions. This variant is present in population databases (rs141292909, gnomAD 0.03%). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 400 of the SRPX2 protein (p.Asn400Ser). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at