NM_015040.4:c.2106C>T

Variant names:

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_015040.4(PIKFYVE):c.2106C>T(p.Pro702Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.972 in 1,611,436 control chromosomes in the GnomAD database, including 762,579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.93 ( 66374 hom., cov: 32)

Exomes 𝑓: 0.98 ( 696205 hom. )

Consequence

PIKFYVE
NM_015040.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.25

Variant links:

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]

PIKFYVE links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP6

Variant 2-208320275-C-T is Benign according to our data. Variant chr2-208320275-C-T is described in ClinVar as [Benign]. Clinvar id is 333898.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-208320275-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.25 with no splicing effect.

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 rank	MANE	Protein	UniProt
PIKFYVE	NM_015040.4 link	c.2106C>T	p.Pro702Pro	synonymous_variant	Exon 17 of 42	ENST00000264380.9	NP_055855.2	Q9Y2I7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
PIKFYVE	ENST00000264380.9 link	c.2106C>T	p.Pro702Pro	synonymous_variant	Exon 17 of 42	1	NM_015040.4	ENSP00000264380.4	Q9Y2I7-1
PIKFYVE	ENST00000443896.5 link	n.*1457C>T		non_coding_transcript_exon_variant	Exon 16 of 19	1		ENSP00000407692.1	F8WEZ0
PIKFYVE	ENST00000443896.5 link	n.*1457C>T		3_prime_UTR_variant	Exon 16 of 19	1		ENSP00000407692.1	F8WEZ0
PIKFYVE	ENST00000452564.1 link	c.1938C>T	p.Pro646Pro	synonymous_variant	Exon 16 of 25	2		ENSP00000405736.1	E9PDH4

Frequencies

GnomAD3 genomes

AF:

0.930

AC:

141484

AN:

152128

Hom.:

66322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.802

Gnomad AMI

AF:

0.996

Gnomad AMR

AF:

0.970

Gnomad ASJ

AF:

0.996

Gnomad EAS

AF:

0.944

Gnomad SAS

AF:

0.932

Gnomad FIN

AF:

0.997

Gnomad MID

AF:

0.975

Gnomad NFE

AF:

0.983

Gnomad OTH

AF:

0.939

GnomAD3 exomes

AF:

0.964

AC:

241037

AN:

249918

Hom.:

116561

AF XY:

0.966

AC XY:

130525

AN XY:

135080

show subpopulations

Gnomad AFR exome

AF:

0.799

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:

1424592

AN:

1459190

Hom.:

696205

Cov.:

AF XY:

0.976

AC XY:

708541

AN XY:

725926

show subpopulations

Gnomad4 AFR exome

AF:

0.796

Gnomad4 AMR exome

AF:

0.982

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:

0.969

GnomAD4 genome

AF:

0.930

AC:

141594

AN:

152246

Hom.:

66374

Cov.:

AF XY:

0.932

AC XY:

69392

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.802

Gnomad4 AMR

AF:

0.970

Gnomad4 ASJ

AF:

0.996

Gnomad4 EAS

AF:

0.944

Gnomad4 SAS

AF:

0.933

Gnomad4 FIN

AF:

0.997

Gnomad4 NFE

AF:

0.983

Gnomad4 OTH

AF:

0.940

Alfa

AF:

0.967

Hom.:

65702

Bravo

AF:

0.922

Asia WGS

AF:

0.931

AC:

3211

AN:

3450

EpiCase

AF:

0.983

EpiControl

AF:

0.985

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Fleck corneal dystrophy

Benign:2

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

BayesDel_noAF

Benign

-0.32

CADD

Benign

8.9

DANN

Benign

0.60

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over