rs34925828
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001384910.1(GUCA1A):c.567C>G(p.Asp189Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. D189D) has been classified as Likely benign.
Frequency
Consequence
NM_001384910.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GUCA1A | NM_001384910.1 | c.567C>G | p.Asp189Glu | missense_variant | 4/4 | ENST00000372958.2 | NP_001371839.1 | |
GUCA1ANB-GUCA1A | NM_000409.5 | c.567C>G | p.Asp189Glu | missense_variant | 6/6 | NP_000400.2 | ||
GUCA1ANB-GUCA1A | NM_001319061.2 | c.567C>G | p.Asp189Glu | missense_variant | 6/6 | NP_001305990.1 | ||
GUCA1ANB-GUCA1A | NM_001319062.2 | c.567C>G | p.Asp189Glu | missense_variant | 5/5 | NP_001305991.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GUCA1A | ENST00000372958.2 | c.567C>G | p.Asp189Glu | missense_variant | 4/4 | 1 | NM_001384910.1 | ENSP00000362049.1 | ||
ENSG00000290147 | ENST00000654459.1 | c.567C>G | p.Asp189Glu | missense_variant | 5/5 | ENSP00000499539.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 22, 2022 | ClinVar contains an entry for this variant (Variation ID: 1360868). This missense change has been observed in individual(s) with retinitis pigmentosa (Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 189 of the GUCA1A protein (p.Asp189Glu). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Not Available"; Align-GVGD: "Not Available". The glutamic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.