chr18-32195471-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005925.3(MEP1B):āc.236T>Cā(p.Leu79Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,082 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 ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L79R) has been classified as Uncertain significance.
Frequency
Consequence
NM_005925.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEP1B | NM_005925.3 | c.236T>C | p.Leu79Pro | missense_variant | 5/15 | ENST00000269202.11 | |
MEP1B | NM_001308171.2 | c.236T>C | p.Leu79Pro | missense_variant | 5/15 | ||
MEP1B | XM_011526013.3 | c.236T>C | p.Leu79Pro | missense_variant | 5/14 | ||
MEP1B | XM_011526014.3 | c.236T>C | p.Leu79Pro | missense_variant | 5/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEP1B | ENST00000269202.11 | c.236T>C | p.Leu79Pro | missense_variant | 5/15 | 1 | NM_005925.3 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455082Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 724180
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2023 | The c.236T>C (p.L79P) alteration is located in exon 5 (coding exon 5) of the MEP1B gene. This alteration results from a T to C substitution at nucleotide position 236, causing the leucine (L) at amino acid position 79 to be replaced by a proline (P). 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