PHLDA3

pleckstrin homology like domain family A member 3

Basic information

Region (hg38): 1:201464278-201469237

Links

ENSG00000174307

∙ NCBI:23612 ∙ OMIM:607054 ∙ HGNC:8934 ∙ Uniprot:Q9Y5J5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PHLDA3 gene.

not_specified (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHLDA3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012396.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHLDA3	protein_coding	protein_coding	ENST00000367311	1	3746

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.250	0.651	125658	0	31	125689	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.150	75	78.8	0.952	0.00000370	802
Missense in Polyphen		26	23.962	1.0851		268
Synonymous	-2.03	55	38.9	1.41	0.00000182	287
Loss of Function	1.21	1	3.41	0.294	1.46e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00142
Finnish	0.00	0.00
European (Non-Finnish)	0.0000274	0.0000264
Middle Eastern	0.00141	0.00142
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: p53/TP53-regulated repressor of Akt/AKT1 signaling. Represses AKT1 by preventing AKT1-binding to membrane lipids, thereby inhibiting AKT1 translocation to the cellular membrane and activation. Contributes to p53/TP53-dependent apoptosis by repressing AKT1 activity. Its direct transcription regulation by p53/TP53 may explain how p53/TP53 can negatively regulate AKT1. May act as a tumor suppressor. {ECO:0000269|PubMed:19203586}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.114
rvis_EVS: 0.17
rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

pHI: 0.0938
hipred: N
hipred_score: 0.354
ghis: 0.498

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Phlda3
Phenotype: embryo phenotype;

Gene ontology

Biological process: anatomical structure morphogenesis;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation of apoptotic process;negative regulation of protein kinase B signaling
Cellular component: cytoplasm;plasma membrane
Molecular function: phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;phosphatidylinositol-5-phosphate binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidylinositol-3,5-bisphosphate binding