rs398123456
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_000528.4(MAN2B1):c.2398G>T(p.Gly800Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,612,740 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G800R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000528.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN2B1 | NM_000528.4 | c.2398G>T | p.Gly800Trp | missense_variant | 20/24 | ENST00000456935.7 | |
MAN2B1 | NM_001173498.2 | c.2395G>T | p.Gly799Trp | missense_variant | 20/24 | ||
MAN2B1 | XM_005259913.3 | c.2401G>T | p.Gly801Trp | missense_variant | 20/24 | ||
MAN2B1 | XM_047438841.1 | c.1297G>T | p.Gly433Trp | missense_variant | 13/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2B1 | ENST00000456935.7 | c.2398G>T | p.Gly800Trp | missense_variant | 20/24 | 1 | NM_000528.4 | A1 | |
MAN2B1 | ENST00000221363.8 | c.2395G>T | p.Gly799Trp | missense_variant | 20/24 | 1 | P4 | ||
MAN2B1 | ENST00000466794.5 | n.2988G>T | non_coding_transcript_exon_variant | 18/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251404Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135894
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460498Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726558
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152242Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74428
ClinVar
Submissions by phenotype
Deficiency of alpha-mannosidase Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | ClinVar Staff, National Center for Biotechnology Information (NCBI) | Jun 07, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at