rs146113445
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The ENST00000356884.11(BICD2):c.1477C>T(p.Arg493Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,611,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R493H) has been classified as Likely benign.
Frequency
Consequence
ENST00000356884.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BICD2 | NM_001003800.2 | c.1477C>T | p.Arg493Cys | missense_variant | 5/7 | ENST00000356884.11 | NP_001003800.1 | |
BICD2 | NM_015250.4 | c.1477C>T | p.Arg493Cys | missense_variant | 5/8 | NP_056065.1 | ||
BICD2 | XM_017014551.2 | c.1558C>T | p.Arg520Cys | missense_variant | 5/8 | XP_016870040.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BICD2 | ENST00000356884.11 | c.1477C>T | p.Arg493Cys | missense_variant | 5/7 | 1 | NM_001003800.2 | ENSP00000349351 | A2 | |
BICD2 | ENST00000375512.3 | c.1477C>T | p.Arg493Cys | missense_variant | 5/8 | 1 | ENSP00000364662 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000843 AC: 21AN: 249066Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134986
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1458790Hom.: 0 Cov.: 32 AF XY: 0.0000455 AC XY: 33AN XY: 725862
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74364
ClinVar
Submissions by phenotype
Autosomal dominant childhood-onset proximal spinal muscular atrophy with contractures Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 26, 2023 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 13, 2020 | The p.R493C variant (also known as c.1477C>T), located in coding exon 5 of the BICD2 gene, results from a C to T substitution at nucleotide position 1477. The arginine at codon 493 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been detected in heterozygous or homozygous state in two members of a family affected with arthrogryposis, developmental delay, and multiple congenital anomalies (Bayram Y et al. J. Clin. Invest., 2016 Feb;126:762-78). However, these individuals were also carriers of a pathogenic variant in another gene and therefore the contribution of this BICD2 variant towards the disease phenotype is uncertain. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 19, 2022 | Observed in both a homozygous and heterozygous state in siblings with joint contractures and multiple congenital anomalies who also harbored other variants related to the phenotype (Bayram Y et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26752647, 28166811) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at