chr22-38129523-C-T

Position:

• chr22-38129523-C-T

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PS1 PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_003560.4(PLA2G6):​c.1117G>A​(p.Gly373Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Synonymous variant affecting the same amino acid position (i.e. G373G) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: PLA2G6 NM_003560.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 7.05

Genes affected

PLA2G6 (HGNC:9039): (phospholipase A2 group VI) The protein encoded by this gene is an A2 phospholipase, a class of enzyme that catalyzes the release of fatty acids from phospholipids. The encoded protein may play a role in phospholipid remodelling, arachidonic acid release, leukotriene and prostaglandin synthesis, fas-mediated apoptosis, and transmembrane ion flux in glucose-stimulated B-cells. Several transcript variants encoding multiple isoforms have been described, but the full-length nature of only three of them have been determined to date. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Pathogenic. Variant got 20 ACMG points.

• PS1: Transcript NM_003560.4 (PLA2G6) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 2863736
• PM1: In a repeat ANK 7 (size 29) in uniprot entity PLPL9_HUMAN there are 11 pathogenic changes around while only 1 benign (92%) in NM_003560.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.99
• PP5: Variant 22-38129523-C-T is Pathogenic according to our data. Variant chr22-38129523-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 159728.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G6	NM_003560.4	c.1117G>A	p.Gly373Arg	missense_variant	8/17	ENST00000332509.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G6	ENST00000332509.8	c.1117G>A	p.Gly373Arg	missense_variant	8/17	1	NM_003560.4	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461770 Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2 AN XY: 727198

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ 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: 0.0000331

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Infantile neuroaxonal dystrophy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Nov 26, 2018	This variant has been reported as either homozygous or in combination with another PLA2G6 variant in individuals affected with infantile neuroaxonal dystrophy or late-onset PLA2G6-associated neurodegeneration (PMID: 19138334, 22934738, 25326637) and segregated with this condition in a family (Invitae external communication). ClinVar contains an entry for this variant (Variation ID: 159728). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with arginine at codon 373 of the PLA2G6 protein (p.Gly373Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine. A mouse model generated by a mutagen that randomly induces point mutations throughout the genome has shown that this missense change results in a significant reduction in calcium responses to ATP in astrocytes (PMID: 19893029, 20947703, 22442204). However, the possibility that there are additional mutations in the neighboring genes of PLA2G6 could not be formally excluded. For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. -
Pathogenic, criteria provided, single submitter	clinical testing	UCLA Clinical Genomics Center, UCLA	Jul 15, 2014	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 22, 2021

The c.1117G>A (p.G373R) alteration is located in exon 8 (coding exon 7) of the PLA2G6 gene. This alteration results from a G to A substitution at nucleotide position 1117, causing the glycine (G) at amino acid position 373 to be replaced by an arginine (R). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). A Chinese patient, reported to have the p.G373R and p.K545E alterations, was diagnosed with infantile neuroaxonal dystrophy. The patient was free of symptoms at birth and achieved normal developmental milestones before onset of symptoms at 7 months, which rapidly progressed to a vegetative state by 5 years. Brain MRI imaging showed cerebellar atrophy and neuropathology showed the typical presence of axonal swelling and spheroid bodies (Wu, 2009). Another Chinese patient with late onset PLA2G6-related neurodegeneration was confirmed to be compound heterozygous with this alteration and the p.I689F alteration based on parental testing. Age of onset was at 14 years with gait disturbance followed by mental and behavioral problems after two years and a brain MRI showing cerebellar atrophy and progressive iron accumulation in the globus pallidus and substantia nigra (Zhang, 2013). The p.G373R alteration was in trans with p.S504L in another Chinese patient with PLA2G6-related neurodegeneration. His brother was also affected but had a milder phenotype (Chen, 2018). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Iron accumulation in brain Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Feb 08, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.57
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.36
CADD	Pathogenic	34
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.71	D;.;.
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D;D;.
M_CAP	Pathogenic	0.41	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Uncertain	0.66	D
MutationAssessor	Uncertain	2.5	M;M;M
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-7.6	D;D;D
REVEL	Pathogenic	0.82
Sift	Pathogenic	0.0	D;D;D
Sift4G	Uncertain	0.0030	D;D;D
Polyphen		1.0	D;D;D
Vest4		0.94
MutPred		0.96		Gain of catalytic residue at G373 (P = 0.0984);Gain of catalytic residue at G373 (P = 0.0984);Gain of catalytic residue at G373 (P = 0.0984);
MVP		0.98
MPC		0.97
ClinPred		1.0	D
GERP RS		5.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.89
gMVP		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs587784327; hg19: chr22-38525530; COSMIC: COSV59269917; COSMIC: COSV59269917;