rs557849165

chr17-10656089-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 20P and 4B. PVS1 PP3_Strong PP5_Very_Strong BS2

The NM_002470.4(MYH3):c.-9+1G>A variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 152,282 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0011 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MYH3 NM_002470.4 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11
• Conservation: PhyloP100: 2.73

Genes affected

MYH3 (HGNC:7573): (myosin heavy chain 3) Myosin is a major contractile protein which converts chemical energy into mechanical energy through the hydrolysis of ATP. Myosin is a hexameric protein composed of a pair of myosin heavy chains (MYH) and two pairs of nonidentical light chains. This gene is a member of the MYH family and encodes a protein with an IQ domain and a myosin head-like domain. Mutations in this gene have been associated with two congenital contracture (arthrogryposis) syndromes, Freeman-Sheldon syndrome and Sheldon-Hall syndrome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 6.7, offset of -13, new splice context is: cagGTggga. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 17-10656089-C-T is Pathogenic according to our data. Variant chr17-10656089-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 587706.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-10656089-C-T is described in Lovd as [Likely_pathogenic]. Variant chr17-10656089-C-T is described in Lovd as [Likely_pathogenic].
• BS2: High AC in GnomAd at 173 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH3	NM_002470.4	c.-9+1G>A		splice_donor_variant		ENST00000583535.6
MYH3	XM_011523870.4	c.-9+1G>A		splice_donor_variant
MYH3	XM_011523871.3	c.-9+1G>A		splice_donor_variant
MYH3	XM_047436127.1	c.-9+1G>A		splice_donor_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH3	ENST00000583535.6	c.-9+1G>A		splice_donor_variant		5	NM_002470.4	P1
MYH3	ENST00000582580.1	n.80+1G>A		splice_donor_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00114 AC: 173 AN: 152164 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00101

Gnomad OTH AF: 0.000956

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 80 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 60

Gnomad4 AFR 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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00114 AC: 173 AN: 152282 Hom.: 0 Cov.: 33 AF XY: 0.00130 AC XY: 97 AN XY: 74472

Gnomad4 AFR AF: 0.0000481

Gnomad4 AMR AF: 0.000588

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00754

Gnomad4 NFE AF: 0.00101

Gnomad4 OTH AF: 0.000946

Alfa AF: 0.00222 Hom.: 0

Bravo AF: 0.000499

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 15, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2023	MYH3: PM3:Strong, PM2:Supporting, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 02, 2023	Published functional studies demonstrate a damaging effect resulting in reduction of translational efficiency (Cameron-Christie et al., 2018); This variant is associated with the following publications: (PMID: 32902138, 34440395, 29805041, 33726816, Sergi2022[casereport], 34204301, 35169139) -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 25, 2024	This variant occurs in a non-coding region of the MYH3 gene. It does not change the encoded amino acid sequence of the MYH3 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs557849165, gnomAD 1.0%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with clinical features of autosomal recessive MYH3-related conditions (PMID: 29805041, 32902138; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 587706). Studies have shown that this variant alters MYH3 gene expression (PMID: 29805041). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 2, but is expected to preserve the integrity of the reading-frame (PMID: 29805041). For these reasons, this variant has been classified as Pathogenic. -

MYH3-related disorder Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Aug 08, 2023	The MYH3 c.-9+1G>A variant results in a substitution at a consensus splice donor site that has been shown to result in abnormal splicing with an increase in transcripts lacking exon 2 (PMID: 29805041). This variant was identified in a compound heterozygous state in at least 9 individuals with spondylocarpotarsal synostosis, multiple pterygium syndrome (MPS), and vertebral fusions, arthrogryposis and multiple pterygia (PMID: 29805041; 34440395; 35169139). The highest frequency of this allele in the Genome Aggregation Database is 0.010640 in the European (Finnish) population, however, this variant is not found in the homozygous state but is flagged as low confidence (version 2.1.1). Functional studies conducted in human cell lines demonstrated that transcripts containing the c.-9+1G>A variant lacking exon 2 display a reduced translational efficiency of 54% compared to wild-type (PMID: 29805041). Based on the available evidence, the c.-9+1G>A variant is classified as likely pathogenic for MYH3-related disorders. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 23, 2022	Variant summary: MYH3 c.-9+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5 prime splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing and results in loss of part of 5'-UTR sequence (Cameron-Christie_2018). The variant allele was found at a frequency of 0.0027 in 31404 control chromosomes. c.-9+1G>A has been reported in the literature and found in our internal database in individuals affected with MYH3-Related Disorders in compound heterozygous or heterozygous status. These reports do not provide unequivocal conclusions about association of the variant with MYH3-Related Disorders. At least one publication reports experimental evidence evaluating an impact on protein function. This variant leads to a translational efficiency of 54% relative to that of the wild-type (Cameron-Christie_2018). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (Pathogenic n=3, VUS n=1, Benign n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Jan 08, 2024	The MYH3 c.-9+1G>A variant is located in the 5' untranslated region. This variant has been reported in the compound heterozygous state in at least six individuals from three different families with autosomal recessive spondylocarpotarsal synostosis syndrome (Cameron-Christie et al 2018. PubMed ID: 29805041). This variant was also detected in the compound heterozygous state in patients with MYH3-associated conditions (Hakonen et al. 2020. PubMed ID: 32902138; Dahan-Oliel et al. 2021. PubMed ID: 34440395; Zhao et al. 2022. PubMed ID: 35169139). In addition, functional evidence supports that this variant results in aberrant splicing and reduced translational efficiency (Cameron-Christie et al 2018. PubMed ID: 29805041). Although this variant has an allele frequency up to 1.1% in Finnish Europeans, this variant is suggested to be a hypomorphic allele. In summary, this variant is interpreted as likely pathogenic. -

Contractures, pterygia, and variable skeletal fusions syndrome 1B Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Feb 27, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	-	- -

Spondylocarpotarsal synostosis syndrome;C1867440:Contractures, pterygia, and spondylocarpotarsal fusion syndrome 1A Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Clinical Genetics Group, University of Otago

Apr 09, 2018

- -

Contractures, pterygia, and spondylocarpotarsal fusion syndrome 1A Pathogenic:1

Pathogenic, no assertion criteria provided

curation

Reproductive Health Research and Development, BGI Genomics

Jan 06, 2020

NG_011537.1(NM_002470.3):c.-9+1G>A in the MYH3 gene has an allele frequency of 0.011 in European(Finnish) subpopulation in the gnomAD database. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. It was detected in multiple individuals with autosomal recessive Spondylocarpotarsal Synostosis Syndrome, compound heterozygous with c.4647+1G>A, c.141T>G, deletion of intron 12 and exon 25 (PMID: 29805041).Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP criteria applied: PVS1; PM3_Strong. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Pathogenic	0.17
Cadd	Pathogenic	27
Dann	Uncertain	0.99

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.86
SpliceAI score (max)		0.92		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.92		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs557849165; hg19: chr17-10559406;