rs764262446

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP2PP3_ModeratePP5

The NM_000540.3(RYR1):ā€‹c.1250T>Cā€‹(p.Leu417Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000132 in 1,439,116 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 Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.000013 ( 0 hom. )

Consequence

RYR1
NM_000540.3 missense

Scores

10
6
2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:7U:2

Conservation

PhyloP100: 5.63
Variant links:
Genes affected
RYR1 (HGNC:10483): (ryanodine receptor 1) This gene encodes a ryanodine receptor found in skeletal muscle. The encoded protein functions as a calcium release channel in the sarcoplasmic reticulum but also serves to connect the sarcoplasmic reticulum and transverse tubule. Mutations in this gene are associated with malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), RYR1. . Gene score misZ 1.918 (greater than the threshold 3.09). Trascript score misZ 3.9788 (greater than threshold 3.09). GenCC has associacion of gene with King-Denborough syndrome, congenital multicore myopathy with external ophthalmoplegia, autosomal recessive centronuclear myopathy, RYR1-related myopathy, lethal multiple pterygium syndrome, malignant hyperthermia of anesthesia, benign Samaritan congenital myopathy, malignant hyperthermia, susceptibility to, 1, congenital myopathy with myasthenic-like onset, central core myopathy.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.938
PP5
Variant 19-38452824-T-C is Pathogenic according to our data. Variant chr19-38452824-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 544398.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Pathogenic=3, Uncertain_significance=2}. Variant chr19-38452824-T-C is described in Lovd as [Likely_pathogenic]. Variant chr19-38452824-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RYR1NM_000540.3 linkuse as main transcriptc.1250T>C p.Leu417Pro missense_variant 13/106 ENST00000359596.8 NP_000531.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RYR1ENST00000359596.8 linkuse as main transcriptc.1250T>C p.Leu417Pro missense_variant 13/1065 NM_000540.3 ENSP00000352608 A2P21817-1
RYR1ENST00000355481.8 linkuse as main transcriptc.1250T>C p.Leu417Pro missense_variant 13/1051 ENSP00000347667 P4P21817-2
RYR1ENST00000599547.6 linkuse as main transcriptc.1250T>C p.Leu417Pro missense_variant, NMD_transcript_variant 13/802 ENSP00000471601

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000434
AC:
9
AN:
207268
Hom.:
0
AF XY:
0.0000355
AC XY:
4
AN XY:
112616
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000268
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000112
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000132
AC:
19
AN:
1439116
Hom.:
0
Cov.:
33
AF XY:
0.00000980
AC XY:
7
AN XY:
714082
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000197
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000999
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756
ExAC
AF:
0.0000248
AC:
3

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:7Uncertain:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

RYR1-related disorder Pathogenic:2
Likely pathogenic, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesSep 18, 2024The RYR1 c.1250T>C variant is predicted to result in the amino acid substitution p.Leu417Pro. This variant was reported in the compound heterozygous state with another RYR1 loss of function variant in at least two individuals with RYR1-related myopathy (See patient 32 in Klein et al. 2011. PubMed ID: 21911697; See case ID 9166 in Supp. Table 2 Marinakis et al. 2021. PubMed ID: 34008892). This variant was also reported in an additional study as compound heterozygous in a patient with pediatric neuromuscular disease, but the second variant was not listed (See Supp. Table 2 in Herman et al. 2020. PubMed ID: 33146414). This variant was found in a patient in a cohort study of RYR1-related congenital myopathies, but no zygosity information was provided (Table 2 and Additional file 4, Fusto. 2022. PubMed ID: 35428369). This variant is reported in 0.027% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as likely pathogenic for autosomal recessive RYR1-related myopathy. -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 26, 2024This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 417 of the RYR1 protein (p.Leu417Pro). This variant is present in population databases (rs764262446, gnomAD 0.03%). This missense change has been observed in individual(s) with autosomal recessive congenital myopathy (PMID: 21911697, 22473935; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 544398). 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 RYR1 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:1Uncertain:1
Pathogenic, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenSep 01, 2020- -
Uncertain significance, criteria provided, single submitterclinical testingRevvity Omics, RevvityJan 05, 2023- -
Congenital multicore myopathy with external ophthalmoplegia Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testing3billionMay 22, 2022The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.004%). The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.96; 3Cnet: 0.97). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000544398). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PMID: 22473935). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
See cases Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingHuman Genetics Bochum, Ruhr University BochumFeb 13, 2023ACMG criteria used to clasify this variant: PP3_STR, PS4_MOD, PM2_SUP -
Central core myopathy Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingLaboratory of Medical Genetics, National & Kapodistrian University of AthensOct 01, 2021PM2, PM3, PP2, PP3 -
Myopathy, RYR1-associated Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpMar 08, 2024Variant summary: RYR1 c.1250T>C (p.Leu417Pro) results in a non-conservative amino acid change in the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.3e-05 in 207268 control chromosomes. c.1250T>C has been reported in the literature in individuals affected with congenital myopathies and central core disease in the compound heterozygous state (Klein_2011, Herman_2021, Rossi_2021, Marinakis_2021, Fusto_2022). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 21911697, 33146414, 33758288, 34008892, 35428369). ClinVar contains an entry for this variant (Variation ID: 544398). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Malignant hyperthermia, susceptibility to, 1 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthSep 23, 2024This missense variant replaces leucine with proline at codon 417 of the RYR1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.85, PMID: 27666373). This variant occurs in the N-terminal region (a.a. 1-552) of the RYR1 protein that is considered to be a hotspot for pathogenic variants that contribute to malignant hyperthermia susceptibility (PMID: 21118704). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with autosomal dominant malignant hyperthermia in the literature, although it is associated with other phenotype(s) (ClinVar variation ID: 544398). This variant has been identified in 9/207268 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Due to insufficient evidence, this variant is classified as a Variant of Uncertain Significance for autosomal dominant malignant hyperthermia. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.31
D
BayesDel_noAF
Pathogenic
0.51
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.81
.;D
Eigen
Uncertain
0.57
Eigen_PC
Uncertain
0.53
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Benign
0.79
T;T
M_CAP
Pathogenic
0.77
D
MetaRNN
Pathogenic
0.94
D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Uncertain
2.4
M;M
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.76
T
PROVEAN
Pathogenic
-4.6
D;D
REVEL
Pathogenic
0.96
Sift
Pathogenic
0.0
D;D
Polyphen
1.0
D;D
Vest4
0.88
MutPred
0.82
Gain of disorder (P = 0.0112);Gain of disorder (P = 0.0112);
MVP
0.99
MPC
1.2
ClinPred
0.83
D
GERP RS
4.3
Varity_R
0.92
gMVP
0.96

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs764262446; hg19: chr19-38943464; API