rs1554842686

Positions:

• chr10-68148354-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000358913.10(MYPN):​c.1132A>C​(p.Ile378Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. I378I) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYPN ENST00000358913.10 missense, splice_region
• Scores: Splicing: ADA: 0.0004196
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.254

Genes affected

MYPN (HGNC:23246): (myopalladin) Striated muscle in vertebrates comprises large proteins which must be organized properly to contract efficiently. Z-lines in striated muscle are a sign of this organization, representing the ends of actin thin filaments, titin, nebulin or nebulette and accessory proteins required for structure and function. This gene encodes a protein which interacts with nebulin in skeletal muscle or nebulette in cardiac muscle and alpha-actinin. In addition, this gene product can interact with a protein with the I-band indicating it has a regulatory as well as structural function. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]

LOC107984240 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10219547).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYPN	NM_032578.4	c.1132A>C	p.Ile378Leu	missense_variant, splice_region_variant	5/20	ENST00000358913.10	NP_115967.2
LOC107984240	XR_001747479.2	n.206-1636T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYPN	ENST00000358913.10	c.1132A>C	p.Ile378Leu	missense_variant, splice_region_variant	5/20	1	NM_032578.4	ENSP00000351790	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 09, 2017

Variant classified as Uncertain Significance - Favor Benign. The p.Ile378Leu var iant in MYPN has not been previously reported in individuals with cardiomyopathy or in large population studies. Isoleucine (Ile) at position 378 is poorly cons erved in mammals and 1 mammal (Armadillo) carries a leucine (Leu) at this positi on, raising the possibility that this change may be tolerated. Additional comput ational prediction tools suggest that the p.Ile378Leu variant may not impact the protein, though this information is not predictive enough to rule out pathogeni city. In summary, while the clinical significance of the p.Ile378Leu variant is uncertain, available data suggest that it is more likely to be benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	13
DANN	Benign	0.79
DEOGEN2	Benign	0.018	.;.;.;T;.
Eigen	Benign	-0.47
Eigen_PC	Benign	-0.32
FATHMM_MKL	Benign	0.56	D
LIST_S2	Benign	0.46	T;T;.;T;T
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.10	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.76	N;.;N;.;N
MutationTaster	Benign	0.99	N;N;N;N
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-0.030	N;N;N;.;N
REVEL	Benign	0.091
Sift	Benign	0.69	T;T;T;.;T
Sift4G	Benign	0.67	T;T;T;T;T
Polyphen		0.0020	B;B;B;.;B
Vest4		0.19
MutPred		0.16		Loss of methylation at K380 (P = 0.0782);.;Loss of methylation at K380 (P = 0.0782);.;Loss of methylation at K380 (P = 0.0782);
MVP		0.56
MPC		0.13
ClinPred		0.080	T
GERP RS		0.26
Varity_R		0.046
gMVP		0.21

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00042
dbscSNV1_RF	Benign	0.050
SpliceAI score (max)		0.030		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: rs1554842686; hg19: chr10-69908111;