chr16-53605610-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015272.5(RPGRIP1L):c.3706C>T(p.Arg1236Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000998 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_015272.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000592 AC: 90AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000546 AC: 137AN: 251036Hom.: 0 AF XY: 0.000649 AC XY: 88AN XY: 135664
GnomAD4 exome AF: 0.00104 AC: 1521AN: 1461718Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 745AN XY: 727166
GnomAD4 genome AF: 0.000591 AC: 90AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74450
ClinVar
Submissions by phenotype
not provided Uncertain:4
- -
- -
Published functional studies suggest a damaging effect; R1236C failed to rescue morpholino phenotype in zebrafish and another study demonstrated impaired binding to EML1 (Khanna et al., 2009; Uzquiano et al., 2019); Observed with a missense variant on the opposite allele (in trans) in a patient with subcortical heterotopia (Uzquiano et al., 2019); Observed in an individual with a clinical diagnosis of Meckel-Gruber syndrome without a second variant in the RPGRIP1L gene identified (Khanna et al., 2009); 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: 19430481, 31390572, 34426522, 36068917, 36061204) -
- -
not specified Uncertain:1
Variant summary: RPGRIP1L c.3706C>T (p.Arg1236Cys) results in a non-conservative amino acid change located in the RPGRIP1, C-terminal domain (IPR041091) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00055 in 251036 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in RPGRIP1L causing Joubert Syndrome And Related Disorders (0.00055 vs 0.00079), allowing no conclusion about variant significance. c.3706C>T has been reported in the literature in an individual with a clinical diagnosis of Meckel syndrome but was heterozygous for this variant (Khanna_2009). Functional assessment for this variant in the zebrafish model was pathogenic (Khanna_2009). In a seperate study the variant impaired subcellular localization and interactions with EML1 (Uzquiano _2019). These reports do not provide unequivocal conclusions about association of the variant with Joubert Syndrome And Related Disorders. Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
RPGRIP1L-related disorder Uncertain:1
The RPGRIP1L c.3706C>T variant is predicted to result in the amino acid substitution p.Arg1236Cys. This variant has been reported in an individual with Meckel syndrome in the absence of a second variant (Khanna et al. 2009. PubMed ID: 19430481) as well as in a fetus with Meckel syndrome in the compound heterozygous state to a likely pathogenic variant (Moreno-Leon et al. 2022. PubMed ID: 36061204). This variant has also been reported in the compound heterozygous state in an individual with subcortical heterotopia (Uzquiano et al. 2019. PubMed ID: 31390572). This variant is reported in 0.095% of alleles in individuals of European (non-Finnish) descent in gnomAD. While we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Uncertain:1
This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1236 of the RPGRIP1L protein (p.Arg1236Cys). This variant is present in population databases (rs151332923, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with clinical features of RPGRIP1L-related conditions and/or Meckel syndrome (PMID: 19430481, 31390572). ClinVar contains an entry for this variant (Variation ID: 235636). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RPGRIP1L protein function. Experimental studies have shown that this missense change affects RPGRIP1L function (PMID: 31390572). 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. -
Joubert syndrome 7 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Meckel syndrome, type 5 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
COACH syndrome 1 Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Meckel syndrome, type 5;C1969053:Joubert syndrome 7;C5436841:COACH syndrome 3 Uncertain:1
- -
Nephronophthisis 8 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Familial aplasia of the vermis Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at