rs864621992
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_000528.4(MAN2B1):c.1063A>C(p.Thr355Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,316 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). Synonymous variant affecting the same amino acid position (i.e. T355T) has been classified as Likely benign.
Frequency
Consequence
NM_000528.4 missense
Scores
Clinical Significance
Conservation
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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.1063A>C | p.Thr355Pro | missense_variant | 8/24 | ENST00000456935.7 | |
MAN2B1 | NM_001173498.2 | c.1060A>C | p.Thr354Pro | missense_variant | 8/24 | ||
MAN2B1 | XM_005259913.3 | c.1066A>C | p.Thr356Pro | missense_variant | 8/24 | ||
MAN2B1 | XM_047438841.1 | c.9-130A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2B1 | ENST00000456935.7 | c.1063A>C | p.Thr355Pro | missense_variant | 8/24 | 1 | NM_000528.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151436Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461880Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727242
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151436Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73902
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