2-208325804-C-G

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2 BP4_Strong BP6_Very_Strong BA1

The NM_015040.4(PIKFYVE):c.2993C>G(p.Thr998Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.972 in 1,613,816 control chromosomes in the GnomAD database, including 764,069 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.93 (66349 hom., cov: 30)
  • Exomes 𝑓: 0.98 (697720 hom.)
• Consequence: PIKFYVE NM_015040.4 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.0190

Genes affected

PIKFYVE (HGNC:23785): (phosphoinositide kinase, FYVE-type zinc finger containing) Phosphorylated derivatives of phosphatidylinositol (PtdIns) regulate cytoskeletal functions, membrane trafficking, and receptor signaling by recruiting protein complexes to cell- and endosomal-membranes. Humans have multiple PtdIns proteins that differ by the degree and position of phosphorylation of the inositol ring. This gene encodes an enzyme (PIKfyve; also known as phosphatidylinositol-3-phosphate 5-kinase type III or PIPKIII) that phosphorylates the D-5 position in PtdIns and phosphatidylinositol-3-phosphate (PtdIns3P) to make PtdIns5P and PtdIns(3,5)biphosphate. The D-5 position also can be phosphorylated by type I PtdIns4P-5-kinases (PIP5Ks) that are encoded by distinct genes and preferentially phosphorylate D-4 phosphorylated PtdIns. In contrast, PIKfyve preferentially phosphorylates D-3 phosphorylated PtdIns. In addition to being a lipid kinase, PIKfyve also has protein kinase activity. PIKfyve regulates endomembrane homeostasis and plays a role in the biogenesis of endosome carrier vesicles from early endosomes. The protein plays a key role in cell entry of ebola virus and SARS-CoV-2 by endocytosis Mutations in this gene cause corneal fleck dystrophy (CFD); an autosomal dominant disorder characterized by numerous small white flecks present in all layers of the corneal stroma. Histologically, these flecks appear to be keratocytes distended with lipid and mucopolysaccharide filled intracytoplasmic vacuoles. [provided by RefSeq, Jul 2021]

ACMG classification

Verdict is Benign. Variant got -19 ACMG points.

• PP2: Missense variant where missense usually causes diseases, PIKFYVE
• BP4: Computational evidence support a benign effect (MetaRNN=1.6278725E-6).
• BP6: Variant 2-208325804-C-G is Benign according to our data. Variant chr2-208325804-C-G is described in ClinVar as [Benign]. Clinvar id is 333910.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-208325804-C-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIKFYVE	NM_015040.4	c.2993C>G	p.Thr998Ser	missense_variant	20/42	ENST00000264380.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIKFYVE	ENST00000264380.9	c.2993C>G	p.Thr998Ser	missense_variant	20/42	1	NM_015040.4	P1
PIKFYVE	ENST00000443896.5	c.*2344C>G		3_prime_UTR_variant, NMD_transcript_variant	19/19	1
PIKFYVE	ENST00000452564.1	c.2825C>G	p.Thr942Ser	missense_variant	19/25	2

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141355 AN: 151888 Hom.: 66297 Cov.: 30

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.939

GnomAD3 exomes AF: 0.965 AC: 241673 AN: 250502 Hom.: 116900 AF XY: 0.966 AC XY: 130943 AN XY: 135492

Gnomad AFR exome AF: 0.800

Gnomad AMR exome AF: 0.985

Gnomad ASJ exome AF: 0.997

Gnomad EAS exome AF: 0.940

Gnomad SAS exome AF: 0.939

Gnomad FIN exome AF: 0.997

Gnomad NFE exome AF: 0.983

Gnomad OTH exome AF: 0.977

GnomAD4 exome AF: 0.976 AC: 1427445 AN: 1461810 Hom.: 697720 Cov.: 77 AF XY: 0.976 AC XY: 709945 AN XY: 727210

Gnomad4 AFR exome AF: 0.797

Gnomad4 AMR exome AF: 0.983

Gnomad4 ASJ exome AF: 0.996

Gnomad4 EAS exome AF: 0.957

Gnomad4 SAS exome AF: 0.941

Gnomad4 FIN exome AF: 0.996

Gnomad4 NFE exome AF: 0.984

Gnomad4 OTH exome AF: 0.970

GnomAD4 genome AF: 0.931 AC: 141465 AN: 152006 Hom.: 66349 Cov.: 30 AF XY: 0.933 AC XY: 69301 AN XY: 74302

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.940

Alfa AF: 0.977 Hom.: 54269

Bravo AF: 0.923

TwinsUK AF: 0.987 AC: 3658

ALSPAC AF: 0.985 AC: 3795

ESP6500AA AF: 0.809 AC: 3564

ESP6500EA AF: 0.982 AC: 8442

ExAC AF: 0.960 AC: 116530

Asia WGS AF: 0.931 AC: 3237 AN: 3478

EpiCase AF: 0.983

EpiControl AF: 0.985

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 28, 2022	- -

Fleck corneal dystrophy Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.81	T
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.97
Dann	Benign	0.29
DEOGEN2	Benign	0.14	T;T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.085	N
LIST_S2	Benign	0.095	T;T
MetaRNN	Benign	0.0000016	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.14	N;.
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-0.10	N;N
REVEL	Benign	0.028
Sift	Benign	0.74	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;B
Vest4		0.025
MutPred		0.36		Loss of phosphorylation at T998 (P = 0.0717);.;
MPC		0.26
ClinPred		0.00051	T
GERP RS		-1.8
Varity_R		0.023
gMVP		0.11

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: rs893253; hg19: chr2-209190528;