rs118192138

Variant names:

• chr19-38572221-T-C
• rs118192138
• NM_000540.3:c.13949T>C

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PP3 PP4 PM2_Supporting PM3

This summary comes from the ClinGen Evidence Repository: The c.13949T>C variant in RYR1 is a missense variant predicted to cause substitution of leucine by proline at amino acid 4650 (p.Leu4650Pro). This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The REVEL computational prediction analysis tool gives a score of 0.805, which is above the threshold of 0.7, evidence that correlates with impact to RYR1 function (PP3). This variant has been detected in two individuals with central core disease (CCD). Of those individuals, both were compound heterozygous for the variant and a VUS and both of those were confirmed in trans by parental testing (RYR1 p.Lys4724Gln, PMID:12937085, PMID:30611313, ClinVar Variation ID: 65957) (PM3). At least one patient with this variant displayed Type I fiber predominance, unique large eccentric cores, few necrotic/regenerative fibers, and connective tissue increase, which is highly specific for RYR1-related myopathy (PP4, PMID:12937085). In summary, the variant meets the criteria to be classified as uncertain significance for autosomal recessive RYR1-related myopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PM2_Supporting, PP3, PM3, PP4 (ClinGen Congenital Myopathies VCEP specifications version 2; 08/27/2024). LINK:https://erepo.genome.network/evrepo/ui/classification/CA024091/MONDO:0100150/150

• Frequency: Genomes: not found (cov: 32)
• Consequence: RYR1 NM_000540.3 missense
• Clinical Significance: Uncertain significance reviewed by expert panel P:3 U:1 O:1
• Conservation: PhyloP100: 5.08

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYR1	NM_000540.3	c.13949T>C	p.Leu4650Pro	missense_variant	Exon 95 of 106	ENST00000359596.8	NP_000531.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR1	ENST00000359596.8	c.13949T>C	p.Leu4650Pro	missense_variant	Exon 95 of 106	5	NM_000540.3	ENSP00000352608.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:3 Uncertain:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:1 Other:1

Apr 06, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Leu4650Pro variant has been previously reported in an affected child who also carried p.Lys4724Gln variant on the other allele (Romero 2003). She was born at 37 weeks of gestation with prenatal history of hydramnion, fetal akinesia and breach presentation. She presented with multiple arthrogryposis, severe hypotonia, amyotrophy and hypomimia, and required respiratory mechanical assistance. Muscle biopsy at two months of age showed type I fiber predominance, unique large eccentric cores, some necrotic or regenerative fibers and connective tissue increase. At age 5, she was reported to have delayed motor development, ptosis and strabismus (Romero 2003). The p.Leu4650Pro variant is listed in ClinVar (Variation ID 65961). Additionally, in vitro functional studies with p.Phe1528Leu demonstrated that this variant results in excitation-contraction uncoupling by reducing channel opening in the absence of a change in calcium ion permeation (Dulhunty et al.) -

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RYR1 database

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

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RYR1-related disorder Pathogenic:1

Jun 03, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Experimental studies have shown that this missense change affects RYR1 function (http://aups.org.au/Proceedings/43/186P/). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 4650 of the RYR1 protein (p.Leu4650Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of autosomal recessive congenital myopathy (PMID: 12937085; externalcommunication). ClinVar contains an entry for this variant (Variation ID: 65961). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on RYR1 protein function. -

Central core myopathy Pathogenic:1

May 11, 2010

GeneReviews

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: curation

- -

RYR1-related myopathy Uncertain:1

Aug 27, 2024

ClinGen Congenital Myopathies Variant Curation Expert Panel, ClinGen

Significance: Uncertain significance

Review Status: reviewed by expert panel

Collection Method: curation

The c.13949T>C variant in RYR1 is a missense variant predicted to cause substitution of leucine by proline at amino acid 4650 (p.Leu4650Pro). This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The REVEL computational prediction analysis tool gives a score of 0.805, which is above the threshold of 0.7, evidence that correlates with impact to RYR1 function (PP3). This variant has been detected in two individuals with central core disease (CCD). Of those individuals, both were compound heterozygous for the variant and a VUS and both of those were confirmed in trans by parental testing (RYR1 p.Lys4724Gln, PMID: 12937085, PMID: 30611313, ClinVar Variation ID: 65957) (PM3). At least one patient with this variant displayed Type I fiber predominance, unique large eccentric cores, few necrotic/regenerative fibers, and connective tissue increase, which is highly specific for RYR1-related myopathy (PP4, PMID: 12937085). In summary, the variant meets the criteria to be classified as uncertain significance for autosomal recessive RYR1-related myopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PM2_Supporting, PP3, PM3, PP4 (ClinGen Congenital Myopathies VCEP specifications version 2; 08/27/2024). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.45
CADD	Uncertain	23
DANN	Benign	0.94
DEOGEN2	Pathogenic	0.93	.;D
Eigen	Uncertain	0.41
Eigen_PC	Uncertain	0.36
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Benign	0.75	T;T
M_CAP	Pathogenic	0.66	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	0.89	D
MutationAssessor	Uncertain	2.5	.;M
PrimateAI	Pathogenic	0.81	D
PROVEAN	Pathogenic	-4.6	D;D
REVEL	Pathogenic	0.81
Sift	Uncertain	0.0020	D;D
Polyphen		0.96	D;D
Vest4		0.93
MutPred		0.93		.;Loss of helix (P = 0.0072);
MVP		0.96
MPC		1.4
ClinPred		0.98	D
GERP RS		5.2
Varity_R		0.87
gMVP		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs118192138; hg19: chr19-39062861;