rs864621991
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_000528.4(MAN2B1):āc.2999T>Cā(p.Phe1000Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,842 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 Likely pathogenic (ā ). Synonymous variant affecting the same amino acid position (i.e. F1000F) 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.2999T>C | p.Phe1000Ser | missense_variant | 24/24 | ENST00000456935.7 | |
MAN2B1 | NM_001173498.2 | c.2996T>C | p.Phe999Ser | missense_variant | 24/24 | ||
MAN2B1 | XM_005259913.3 | c.3002T>C | p.Phe1001Ser | missense_variant | 24/24 | ||
MAN2B1 | XM_047438841.1 | c.1898T>C | p.Phe633Ser | missense_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2B1 | ENST00000456935.7 | c.2999T>C | p.Phe1000Ser | missense_variant | 24/24 | 1 | NM_000528.4 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251484Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727228
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Deficiency of alpha-mannosidase Pathogenic:1Uncertain:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Aug 01, 2023 | - - |
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