rs372999773

Variant names:

• chr14-20461232-C-A
• NM_144568.4:c.94G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-20461232-C-A
• chr14-20461232-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.94G>T​(p.Ala32Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000902 in 1,108,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 9.0e-7 (0 hom.)
• Consequence: PIP4P1 NM_144568.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957

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=0.21423101).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIP4P1	NM_144568.4	c.94G>T	p.Ala32Ser	missense_variant	Exon 1 of 7	ENST00000250489.9	NP_653169.2
PIP4P1	NM_001100814.3	c.94G>T	p.Ala32Ser	missense_variant	Exon 1 of 7		NP_001094284.1
PIP4P1	XM_024449739.2	c.94G>T	p.Ala32Ser	missense_variant	Exon 1 of 6		XP_024305507.1
PIP4P1	XM_024449740.2	c.94G>T	p.Ala32Ser	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.94G>T	p.Ala32Ser	missense_variant	Exon 1 of 7	1	NM_144568.4	ENSP00000250489.4
PIP4P1	ENST00000398020.6	c.94G>T	p.Ala32Ser	missense_variant	Exon 1 of 7	1		ENSP00000381102.4
PIP4P1	ENST00000557041.1	n.170G>T		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 9.02e-7 AC: 1 AN: 1108818 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 525842

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: 0.0000309

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.064
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	18
DANN	Benign	0.95
DEOGEN2	Benign	0.032	T;.
Eigen	Benign	0.15
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.59	T;T
M_CAP	Benign	0.0089	T
MetaRNN	Benign	0.21	T;T
MetaSVM	Benign	-0.97	T
PrimateAI	Uncertain	0.60	T
PROVEAN	Benign	-0.22	N;N
REVEL	Benign	0.24
Sift	Benign	0.38	T;T
Sift4G	Benign	0.83	T;T
Polyphen		0.98	D;D
Vest4		0.15
MutPred		0.41		Gain of catalytic residue at S30 (P = 0);Gain of catalytic residue at S30 (P = 0);
MVP		0.068
MPC		0.52
ClinPred		0.60	D
GERP RS		3.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.043
gMVP		0.17

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-20929391;