PHLDB2

pleckstrin homology like domain family B member 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 3:111732496-111976517

Links

ENSG00000144824 ∙ NCBI:90102 ∙ OMIM:610298 ∙ HGNC:29573 ∙ Uniprot:Q86SQ0 ∙ 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 PHLDB2 gene.

• Inborn genetic diseases (52 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHLDB2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			51	1	5	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	51	1	7

Variants in PHLDB2

This is a list of pathogenic ClinVar variants found in the PHLDB2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-111732624-G-A		not specified	Likely benign (Mar 06, 2023)
3-111845896-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-111884132-G-C		not specified	Uncertain significance (Oct 10, 2023)
3-111884187-G-A		not specified	Uncertain significance (Jun 06, 2023)
3-111884189-C-G		not specified	Uncertain significance (May 17, 2023)
3-111884208-C-T		not specified	Uncertain significance (May 17, 2023)
3-111884214-G-T			Benign (Apr 04, 2018)
3-111884370-G-A		not specified	Uncertain significance (Jan 29, 2024)
3-111884405-C-G		not specified	Uncertain significance (Jan 24, 2024)
3-111884405-C-T		not specified	Uncertain significance (Aug 30, 2022)
3-111884453-G-A		not specified	Uncertain significance (Jun 30, 2023)
3-111884471-A-G		not specified	Uncertain significance (Jun 16, 2023)
3-111884478-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-111884483-A-G		not specified	Uncertain significance (Dec 27, 2023)
3-111884508-A-T		not specified	Uncertain significance (Nov 10, 2022)
3-111884551-T-A		not specified	Uncertain significance (Jan 27, 2022)
3-111884612-A-G		not specified	Uncertain significance (Dec 15, 2022)
3-111884649-C-T			Benign (Jun 05, 2018)
3-111884693-A-C		not specified	Uncertain significance (May 04, 2022)
3-111884710-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-111884729-G-T		not specified	Uncertain significance (Nov 08, 2022)
3-111884730-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-111884751-G-C		not specified	Uncertain significance (Oct 27, 2021)
3-111884760-A-G		not specified	Uncertain significance (Mar 01, 2023)
3-111884943-A-G		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHLDB2	protein_coding	protein_coding	ENST00000431670	17	244021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-8	1.00	125661	0	87	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.376	650	678	0.959	0.0000367	8277
Missense in Polyphen		164	181.05	0.90585		2141
Synonymous	-0.674	261	248	1.05	0.0000130	2367
Loss of Function	4.01	23	55.1	0.417	0.00000297	706

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000418	0.000418
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000281	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000407	0.000404
Middle Eastern	0.000281	0.000272
South Asian	0.000497	0.000490
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be involved in the assembly of the postsynaptic apparatus. May play a role in acetyl-choline receptor (AChR) aggregation in the postsynaptic membrane (By similarity). {ECO:0000250, ECO:0000269|PubMed:12376540}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in muscle cell - TarBase;Regulation of Microtubule Cytoskeleton;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.801
• rvis_EVS: 0.48
• rvis_percentile_EVS: 78.88

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.372
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phldb2

Gene ontology

• Biological process: microtubule cytoskeleton organization;regulation of gastrulation;regulation of epithelial to mesenchymal transition;establishment of protein localization;negative regulation of stress fiber assembly;negative regulation of focal adhesion assembly;regulation of microtubule cytoskeleton organization;negative regulation of wound healing, spreading of epidermal cells;positive regulation of basement membrane assembly involved in embryonic body morphogenesis
• Cellular component: cytosol;plasma membrane;focal adhesion;cell leading edge;intermediate filament cytoskeleton;basal cortex
• Molecular function: protein binding;cadherin binding