rs201822068
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The ENST00000371974.8(SURF1):āc.893C>Gā(p.Pro298Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000111 in 1,613,728 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P298L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000371974.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SURF1 | NM_003172.4 | c.893C>G | p.Pro298Arg | missense_variant | 9/9 | ENST00000371974.8 | NP_003163.1 | |
SURF1 | NM_001280787.1 | c.566C>G | p.Pro189Arg | missense_variant | 8/8 | NP_001267716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SURF1 | ENST00000371974.8 | c.893C>G | p.Pro298Arg | missense_variant | 9/9 | 1 | NM_003172.4 | ENSP00000361042 | P1 | |
SURF1 | ENST00000615505.4 | c.566C>G | p.Pro189Arg | missense_variant | 8/8 | 1 | ENSP00000482067 | |||
SURF1 | ENST00000437995.1 | n.803C>G | non_coding_transcript_exon_variant | 8/8 | 5 | |||||
SURF1 | ENST00000495952.5 | n.883C>G | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250288Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135422
GnomAD4 exome AF: 0.000113 AC: 165AN: 1461410Hom.: 0 Cov.: 33 AF XY: 0.0000935 AC XY: 68AN XY: 726934
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74482
ClinVar
Submissions by phenotype
Leigh syndrome Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 16, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 21, 2022 | This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 298 of the SURF1 protein (p.Pro298Arg). This variant is present in population databases (rs201822068, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with SURF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 526791). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.893C>G (p.P298R) alteration is located in exon 9 (coding exon 9) of the SURF1 gene. This alteration results from a C to G substitution at nucleotide position 893, causing the proline (P) at amino acid position 298 to be replaced by an arginine (R). 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