PHLDB1

pleckstrin homology like domain family B member 1, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 11:118606440-118658031

Links

ENSG00000019144 ∙ NCBI:23187 ∙ OMIM:612834 ∙ HGNC:23697 ∙ Uniprot:Q86UU1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Osteogenesis imperfecta, type XXIII	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	36543534
The use of bisphosphonates has been described as beneficial

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PHLDB1 gene.

• not_specified (172 variants)
• not_provided (8 variants)
• Osteogenesis_imperfecta,_type_23 (2 variants)
• Diamond-Blackfan_anemia_9 (1 variants)
• Bardet-Biedl_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHLDB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001144758.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			173	4		177
nonsense						0
start loss						0
frameshift	2					2
splice donor/acceptor (+/-2bp)						0
Total	2	0	173	7	1

Highest pathogenic variant AF is 6.84085e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHLDB1	protein_coding	protein_coding	ENST00000361417	22	51587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.107	0.893	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	732	853	0.858	0.0000558	8763
Missense in Polyphen		212	268.52	0.78952		2674
Synonymous	0.726	316	333	0.949	0.0000189	2991
Loss of Function	5.53	15	62.0	0.242	0.00000349	676

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000178
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.650
• rvis_EVS: -1.85
• rvis_percentile_EVS: 2.05

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.614
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phldb1

Gene ontology

• Biological process: regulation of gastrulation;regulation of epithelial to mesenchymal transition;regulation of microtubule cytoskeleton organization;positive regulation of basement membrane assembly involved in embryonic body morphogenesis
• Cellular component: basal cortex