rs1308457468

Variant names:

• chr14-20461276-C-G
• rs1308457468
• NM_144568.4:c.50G>C

Your query was ambiguous. Multiple possible variants found:

• chr14-20461276-C-G
• chr14-20461276-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_144568.4(PIP4P1):​c.50G>C​(p.Gly17Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
• Consequence: PIP4P1 NM_144568.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.38

Genes affected

PIP4P1 (HGNC:19299): (phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1) TMEM55B catalyzes the degradation of phosphatidylinositol 4,5-bisphosphate (PtdIns-4,5-P2) by removing the 4-phosphate (Ungewickell et al., 2005 [PubMed 16365287]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1447413).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIP4P1	NM_144568.4	c.50G>C	p.Gly17Ala	missense_variant	Exon 1 of 7	ENST00000250489.9	NP_653169.2
PIP4P1	NM_001100814.3	c.50G>C	p.Gly17Ala	missense_variant	Exon 1 of 7		NP_001094284.1
PIP4P1	XM_024449739.2	c.50G>C	p.Gly17Ala	missense_variant	Exon 1 of 6		XP_024305507.1
PIP4P1	XM_024449740.2	c.50G>C	p.Gly17Ala	missense_variant	Exon 1 of 6		XP_024305508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIP4P1	ENST00000250489.9	c.50G>C	p.Gly17Ala	missense_variant	Exon 1 of 7	1	NM_144568.4	ENSP00000250489.4
PIP4P1	ENST00000398020.6	c.50G>C	p.Gly17Ala	missense_variant	Exon 1 of 7	1		ENSP00000381102.4
PIP4P1	ENST00000557041.1	n.126G>C		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152220 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152220 Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1 AN XY: 74366

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.031	T
BayesDel_noAF	Benign	-0.28
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.034	T;.
Eigen	Benign	0.18
Eigen_PC	Uncertain	0.22
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.75	T;T
M_CAP	Benign	0.049	D
MetaRNN	Benign	0.14	T;T
MetaSVM	Benign	-0.59	T
PrimateAI	Pathogenic	0.79	T
PROVEAN	Benign	0.070	N;N
REVEL	Benign	0.10
Sift	Benign	0.18	T;T
Sift4G	Benign	0.70	T;T
Polyphen		0.076	B;D
Vest4		0.20
MutPred		0.55		Gain of catalytic residue at A19 (P = 0);Gain of catalytic residue at A19 (P = 0);
MVP		0.18
MPC		1.1
ClinPred		0.85	D
GERP RS		3.8
Varity_R		0.19
gMVP		0.43

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: rs1308457468; hg19: chr14-20929435;