19-7535576-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The ENST00000221249.10(PNPLA6):c.26T>C(p.Met9Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,452,596 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: PNPLA6 ENST00000221249.10 missense, splice_region
• Scores: Splicing: ADA: 0.9196
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.656

Genes affected

PNPLA6 (HGNC:16268): (patatin like phospholipase domain containing 6) This gene encodes a phospholipase that deacetylates intracellular phosphatidylcholine to produce glycerophosphocholine. It is thought to function in neurite outgrowth and process elongation during neuronal differentiation. The protein is anchored to the cytoplasmic face of the endoplasmic reticulum in both neurons and non-neuronal cells. Mutations in this gene result in autosomal recessive spastic paraplegia, and the protein is the target for neurodegeneration induced by organophosphorus compounds and chemical warfare agents. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, PNPLA6
• BP4: Computational evidence support a benign effect (MetaRNN=0.23395485).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNPLA6	NM_001166111.2	c.26T>C	p.Met9Thr	missense_variant, splice_region_variant	2/34
PNPLA6	NM_001166113.1	c.26T>C	p.Met9Thr	missense_variant, splice_region_variant	3/35
PNPLA6	NM_006702.5	c.26T>C	p.Met9Thr	missense_variant, splice_region_variant	3/35
PNPLA6	NM_001166112.2	c.26T>C	p.Met9Thr	missense_variant, splice_region_variant	3/34

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNPLA6	ENST00000221249.10	c.26T>C	p.Met9Thr	missense_variant, splice_region_variant	3/35	1		A1
PNPLA6	ENST00000450331.7	c.26T>C	p.Met9Thr	missense_variant, splice_region_variant	3/35	1		A1
PNPLA6	ENST00000414982.7	c.26T>C	p.Met9Thr	missense_variant, splice_region_variant	2/34	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000344 AC: 5 AN: 1452596 Hom.: 0 Cov.: 31 AF XY: 0.00000416 AC XY: 3 AN XY: 721624

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000386

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000271

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary spastic paraplegia 39 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Aug 23, 2023

This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 9 of the PNPLA6 protein (p.Met9Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PNPLA6-related conditions. ClinVar contains an entry for this variant (Variation ID: 2202447). 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.076	T
BayesDel_noAF	Benign	-0.35
Cadd	Benign	21
Dann	Uncertain	0.99
Eigen	Benign	-0.072
Eigen_PC	Benign	0.031
FATHMM_MKL	Benign	0.49	N
M_CAP	Benign	0.060	D
MetaRNN	Benign	0.18	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.90	T
MutationTaster	Benign	0.53	N;N;N;N
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-1.7	N;.;.;N;.;N;N;.;.
REVEL	Benign	0.092
Sift	Benign	0.048	D;.;.;D;.;D;D;.;.
Sift4G	Benign	0.57	T;T;T;T;T;D;T;T;T
Polyphen		0.087	B;.;.;.;.;.;B;.;.
Vest4		0.37
MutPred		0.23		Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);Gain of glycosylation at M9 (P = 0.0137);
MVP		0.42
MPC		1.4
ClinPred		0.97	D
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.7
Varity_R		0.82
gMVP		0.51

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.92
dbscSNV1_RF	Pathogenic	0.75
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-7600462;