PHLDB3

pleckstrin homology like domain family B member 3, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 19:43474953-43504935

Links

ENSG00000176531 ∙ NCBI:653583 ∙ ∙ HGNC:30499 ∙ Uniprot:Q6NSJ2 ∙ 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 PHLDB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHLDB3 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				1	1	2
missense			46	3	2	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	46	4	3

Variants in PHLDB3

This is a list of pathogenic ClinVar variants found in the PHLDB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43475423-T-C		not specified	Uncertain significance (Mar 25, 2024)
19-43475480-G-A		not specified	Uncertain significance (Feb 10, 2023)
19-43478054-G-T		not specified	Uncertain significance (May 31, 2023)
19-43478061-G-A			Benign (Dec 18, 2018)
19-43478082-C-T		not specified	Uncertain significance (Oct 27, 2023)
19-43478120-G-T		not specified	Uncertain significance (Aug 16, 2022)
19-43479383-A-T		not specified	Uncertain significance (Jul 17, 2023)
19-43479455-T-C		not specified	Uncertain significance (Dec 28, 2022)
19-43479502-G-T		not specified	Uncertain significance (Dec 03, 2021)
19-43479588-T-G			Likely benign (Dec 31, 2019)
19-43479589-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-43479589-G-C		not specified	Uncertain significance (Nov 16, 2022)
19-43479601-G-T			Likely benign (Jul 10, 2018)
19-43486286-G-A		not specified	Uncertain significance (Nov 14, 2023)
19-43486297-C-A		not specified	Uncertain significance (Jul 05, 2023)
19-43486610-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-43486637-G-A		not specified	Uncertain significance (May 23, 2023)
19-43486644-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-43486692-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-43486790-G-A		not specified	Uncertain significance (Jun 07, 2023)
19-43486850-G-T		not specified	Uncertain significance (Jul 12, 2022)
19-43486862-C-T		not specified	Uncertain significance (Oct 25, 2023)
19-43486867-G-T			Likely benign (Nov 27, 2018)
19-43487047-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-43487051-G-A		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHLDB3	protein_coding	protein_coding	ENST00000292140	15	29982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.62e-21	0.00443	125333	3	272	125608	0.00110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.399	414	392	1.06	0.0000250	3993
Missense in Polyphen		121	115.59	1.0468		1199
Synonymous	-0.0149	151	151	1.00	0.00000831	1302
Loss of Function	0.419	33	35.7	0.924	0.00000197	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00255	0.00255
Ashkenazi Jewish	0.000384	0.000298
East Asian	0.000349	0.000326
Finnish	0.0000493	0.0000462
European (Non-Finnish)	0.000542	0.000511
Middle Eastern	0.000349	0.000326
South Asian	0.00404	0.00380
Other	0.00124	0.00114

dbNSFP

Source: dbNSFP

• Pathway: TCR (Consensus)

Intolerance Scores

• loftool: 0.967
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.52

Haploinsufficiency Scores

• pHI: 0.211
• hipred: N
• hipred_score: 0.144
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0900

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phldb3

Gene ontology

• Molecular function: enzyme binding