chr22-19724183-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP5_Moderate
The NM_000407.5(GP1BB):c.340C>T(p.Arg114Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000159 in 1,256,846 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_000407.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GP1BB | NM_000407.5 | c.340C>T | p.Arg114Cys | missense_variant | Exon 2 of 2 | ENST00000366425.4 | NP_000398.1 | |
SEPT5-GP1BB | NR_037611.1 | n.4080C>T | non_coding_transcript_exon_variant | Exon 12 of 12 | ||||
SEPT5-GP1BB | NR_037612.1 | n.2584C>T | non_coding_transcript_exon_variant | Exon 12 of 12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GP1BB | ENST00000366425.4 | c.340C>T | p.Arg114Cys | missense_variant | Exon 2 of 2 | 1 | NM_000407.5 | ENSP00000383382.2 | ||
ENSG00000284874 | ENST00000455843.5 | n.*1425C>T | non_coding_transcript_exon_variant | Exon 12 of 12 | 1 | ENSP00000391731.1 | ||||
ENSG00000284874 | ENST00000455843.5 | n.*1425C>T | 3_prime_UTR_variant | Exon 12 of 12 | 1 | ENSP00000391731.1 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150660Hom.: 0 Cov.: 33
GnomAD4 exome AF: 9.04e-7 AC: 1AN: 1106186Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 532678
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150660Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73532
ClinVar
Submissions by phenotype
Bernard-Soulier syndrome, type B Pathogenic:1
- -
GP1BB-related disorder Uncertain:1
The GP1BB c.340C>T variant is predicted to result in the amino acid substitution p.Arg114Cys. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at