rs373741350

Positions:

• chr1-15719900-C-G
• chr1-15719900-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_015164.4(PLEKHM2):​c.632C>G​(p.Ala211Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A211T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: PLEKHM2 NM_015164.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.66

Genes affected

PLEKHM2 (HGNC:29131): (pleckstrin homology and RUN domain containing M2) This gene encodes a protein that binds the plus-end directed microtubule motor protein kinesin, together with the lysosomal GTPase Arl8, and is required for lysosomes to distribute away from the microtubule-organizing center. The encoded protein belongs to the multisubunit BLOC-one-related complex that regulates lysosome positioning. It binds a Salmonella effector protein called Salmonella induced filament A and is a critical host determinant in Salmonella pathogenesis. It has a domain architecture consisting of an N-terminal RPIP8, UNC-14, and NESCA (RUN) domain that binds kinesin-1 as well as the lysosomal GTPase Arl8, and a C-terminal pleckstrin homology domain that binds the Salmonella induced filament A effector protein. Naturally occurring mutations in this gene lead to abnormal localization of lysosomes, impaired autophagy flux and are associated with recessive dilated cardiomyopathy and left ventricular noncompaction. [provided by RefSeq, Feb 2017]

PLEKHM2 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.34155035).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLEKHM2	NM_015164.4	c.632C>G	p.Ala211Gly	missense_variant	6/20	ENST00000375799.8	NP_055979.2
PLEKHM2	NM_001410755.1	c.632C>G	p.Ala211Gly	missense_variant	6/19		NP_001397684.1
PLEKHM2	XM_017000757.1	c.671C>G	p.Ala224Gly	missense_variant	6/20		XP_016856246.1
PLEKHM2	XM_017000758.1	c.671C>G	p.Ala224Gly	missense_variant	6/19		XP_016856247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLEKHM2	ENST00000375799.8	c.632C>G	p.Ala211Gly	missense_variant	6/20	1	NM_015164.4	ENSP00000364956.3
PLEKHM2	ENST00000375793.2	c.632C>G	p.Ala211Gly	missense_variant	6/19	5		ENSP00000364950.2
PLEKHM2	ENST00000642363.1	c.632C>G	p.Ala211Gly	missense_variant	6/21			ENSP00000494591.1
PLEKHM2	ENST00000462455.1	n.*31C>G		downstream_gene_variant		5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.91
BayesDel_addAF	Uncertain	0.038	T
BayesDel_noAF	Benign	-0.18
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.11	T;.;.
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.96	D;D;D
M_CAP	Benign	0.032	D
MetaRNN	Benign	0.34	T;T;T
MetaSVM	Benign	-0.81	T
MutationAssessor	Uncertain	2.1	M;.;.
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-0.56	N;N;.
REVEL	Benign	0.19
Sift	Uncertain	0.013	D;D;.
Sift4G	Uncertain	0.038	D;T;.
Polyphen		0.98	D;.;.
Vest4		0.58
MutPred		0.14		Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);
MVP		0.66
MPC		0.39
ClinPred		0.84	D
GERP RS		5.5
Varity_R		0.60
gMVP		0.55

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: rs373741350; hg19: chr1-16046395;