rs201588259

chr19-38517469-A-Cchr19-38517469-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2 BP6

The NM_000540.3(RYR1):c.9796A>C(p.Met3266Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M3266T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: RYR1 NM_000540.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:5 B:2
• Conservation: PhyloP100: 9.27

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 0 ACMG points.

• PP2: Missense variant where missense usually causes diseases, RYR1
• BP6: Variant 19-38517469-A-C is Benign according to our data. Variant chr19-38517469-A-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 478302.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=5}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR1	NM_000540.3	c.9796A>C	p.Met3266Leu	missense_variant	66/106	ENST00000359596.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR1	ENST00000359596.8	c.9796A>C	p.Met3266Leu	missense_variant	66/106	5	NM_000540.3	A2
RYR1	ENST00000355481.8	c.9796A>C	p.Met3266Leu	missense_variant	66/105	1		P4
RYR1	ENST00000594335.5	c.*539A>C		3_prime_UTR_variant, NMD_transcript_variant	26/49	1
RYR1	ENST00000599547.6	c.*555A>C		3_prime_UTR_variant, NMD_transcript_variant	65/80	2

Frequencies

GnomAD3 genomes AF: 0.000105 AC: 16 AN: 152026 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.000480

GnomAD3 exomes AF: 0.000112 AC: 28 AN: 250522 Hom.: 0 AF XY: 0.000111 AC XY: 15 AN XY: 135556

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000202

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000159

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000116 AC: 169 AN: 1461872 Hom.: 0 Cov.: 34 AF XY: 0.000114 AC XY: 83 AN XY: 727238

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.000157

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.000131

Gnomad4 OTH exome AF: 0.000132

GnomAD4 genome AF: 0.0000986 AC: 15 AN: 152144 Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8 AN XY: 74372

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.000475

Alfa AF: 0.000176 Hom.: 0

Bravo AF: 0.000110

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000824 AC: 10

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.000491

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:5 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1 Benign:2

Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 31, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 30, 2021	This variant is associated with the following publications: (PMID: 29635721) -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	RYR1: PP3, BS2 -

Malignant hyperthermia, susceptibility to, 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Feb 05, 2024

This missense variant replaces methionine with leucine at codon 3266 of the RYR1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two individuals affected with neuromuscular conditions, one individual was found to be malignant hyperthermia susceptible and one individual was found to be malignant hyperthermia normal (PMID: 29635721, 36283893). This variant has been identified in 33/281826 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

RYR1-related myopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Molecular Genetics, Royal Melbourne Hospital

Feb 05, 2024

This sequence change in RYR1 is predicted to replace methionine with leucine at codon 3266, p.(Met3266Leu). The methionine residue is highly conserved (100 vertebrates, Multiz Alignments), and is located in exon 66 in the cytoplasmic domain. There is a small physicochemical difference between methionine and leucine. The highest population minor allele frequency in the population database gnomAD v4.0 is 0.01% (155/1,179,982 alleles) in the European (non-Finnish) population, which is consistent with recessive disease. This variant has been classified as likely benign or as a variant of uncertain significance (ClinVar ID: 478302). The variant has been detected in at least two individuals with malignant hyperthermia (MH) susceptibility and one individual MH negative by in vitro muscle contracture testing, with variable muscle disease features (PMID: 29635721, 36283893; Royal Melbourne Hospital). Computational evidence is uninformative for the missense substitution (REVEL = 0.55). Based on the classification scheme RMH ACMG Guidelines v1.6.1, this variant is classified as a VARIANT of UNCERTAIN SIGNIFICANCE. Following criteria is met: PM2_Supporting. -

Congenital myasthenic syndrome 12 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

MGZ Medical Genetics Center

Feb 25, 2022

- -

RYR1-Related Disorders Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Aug 10, 2022

This sequence change replaces methionine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 3266 of the RYR1 protein (p.Met3266Leu). This variant is present in population databases (rs201588259, gnomAD 0.02%). This missense change has been observed in individual(s) with myalgia and elevated creatine kinase levels (PMID: 29635721). ClinVar contains an entry for this variant (Variation ID: 478302). 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 not expected to disrupt RYR1 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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.45
BayesDel_addAF	Benign	-0.052	T
BayesDel_noAF	Uncertain	-0.040
Cadd	Benign	20
Dann	Benign	0.41
Eigen	Uncertain	0.27
Eigen_PC	Benign	0.22
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.92	D;D
M_CAP	Uncertain	0.24	D
MetaRNN	Uncertain	0.60	D;D
MetaSVM	Uncertain	0.40	D
MutationAssessor	Uncertain	2.6	M;M
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.81	D
PROVEAN	Benign	-2.0	N;N
REVEL	Uncertain	0.55
Sift	Benign	0.23	T;T
Polyphen		0.65	P;P
Vest4		0.63
MutPred		0.31		Loss of phosphorylation at Y3263 (P = 0.0917);Loss of phosphorylation at Y3263 (P = 0.0917);
MVP		0.93
MPC		0.29
ClinPred		0.38	T
GERP RS		4.0
Varity_R		0.47
gMVP		0.56

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: rs201588259; hg19: chr19-39008109;