rs869025197
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_006912.6(RIT1):c.265T>C(p.Tyr89His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,742 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 Pathogenic (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
RIT1
NM_006912.6 missense
NM_006912.6 missense
Scores
13
5
1
Clinical Significance
Conservation
PhyloP100: 7.55
Genes affected
RIT1 (HGNC:10023): (Ras like without CAAX 1) This gene encodes a member of a subfamily of Ras-related GTPases. The encoded protein is involved in regulating p38 MAPK-dependent signaling cascades related to cellular stress. This protein also cooperates with nerve growth factor to promote neuronal development and regeneration. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PM1
?
In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in NM_006912.6
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.961
PP5
?
Variant 1-155904475-A-G is Pathogenic according to our data. Variant chr1-155904475-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 183411.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-155904475-A-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIT1 | NM_006912.6 | c.265T>C | p.Tyr89His | missense_variant | 5/6 | ENST00000368323.8 | |
RIT1 | NM_001256821.2 | c.316T>C | p.Tyr106His | missense_variant | 5/6 | ||
RIT1 | NM_001256820.2 | c.157T>C | p.Tyr53His | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIT1 | ENST00000368323.8 | c.265T>C | p.Tyr89His | missense_variant | 5/6 | 1 | NM_006912.6 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461742Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727144
GnomAD4 exome
AF:
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1
AN:
1461742
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Cov.:
31
AF XY:
AC XY:
1
AN XY:
727144
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Noonan syndrome 8 Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 27, 2023 | This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 89 of the RIT1 protein (p.Tyr89His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Noonan syndrome (PMID: 23791108, 26757980; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 183411). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is not expected to disrupt RIT1 function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects RIT1 function (PMID: 26714497, 27226556). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Aug 01, 2022 | PS3, PS4_Moderate, PM1, PM2, PP3 - |
RIT1-related condition Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 27, 2023 | The RIT1 c.316T>C variant is predicted to result in the amino acid substitution p.Tyr106His. This variant is also referred to as c.265T>C (p.Tyr89His) in an alternate transcript (NM_006912). This variant has been identified in the heterozygous state in an individual with Noonan syndrome or a related phenotype (Aoki et al. 2013. PubMed ID: 23791108; Cavé et al. 2016. PubMed ID: 26757980). Functional studies determined that the p.Tyr106His variant leads to enhanced activation and a more rapid nucleotide exchange rate as compared to wildtype (Fang et al. 2016. PubMed ID: 27226556; Yaoita et al. 2016. PubMed ID: 26714497). To our knowledge, this variant has not been reported in a large population database, indicating this variant is rare. In the ClinVar database, this variant is interpreted as pathogenic by multiple outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/183411/). This variant is interpreted as pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 28, 2017 | The Y89H variant has been published in patients diagnosed with a disorder in the Noonan syndrome spectrum (Aoki et al., 2013; Aoki et al., 2015). In vitro functional studies have demonstrated that the Y89H variant causes enhanced Elk1 transactivation and a 4-fold faster nucleotide exchange rate in comparison to wild-type (Fang et al., 2016; Yaoita et al., 2016). The Y89H variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The Y89H variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. Pathogenic variants in an adjacent residue (M90I/V) and nearby residues (A84V) have been reported in the Human Gene Mutation Database in association with Noonan Syndrome (Stenson et al., 2014), supporting the functional importance of this region of the protein. - |
Noonan syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Service de Génétique Moléculaire, Hôpital Robert Debré | - | - - |
Noonan syndrome and Noonan-related syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Dec 02, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;T;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;.
REVEL
Pathogenic
Sift
Pathogenic
D;D;D;.
Sift4G
Pathogenic
D;D;D;.
Polyphen
D;.;.;.
Vest4
MutPred
Gain of disorder (P = 0.0293);.;.;Gain of disorder (P = 0.0293);
MVP
MPC
2.1
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at