PBLD

phenazine biosynthesis like protein domain containing

Basic information

Region (hg38): 10:68282659-68333049

Links

ENSG00000108187 ∙ NCBI:64081 ∙ OMIM:612189 ∙ HGNC:23301 ∙ Uniprot:P30039 ∙ 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 PBLD gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBLD 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						0
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in PBLD

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

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

Position	Type	Phenotype	Significance	ClinVar
10-68284217-C-G		not specified	Uncertain significance (Aug 08, 2023)
10-68284236-C-T		not specified	Uncertain significance (Feb 15, 2023)
10-68285357-C-G		not specified	Uncertain significance (Sep 25, 2023)
10-68285377-G-A		not specified	Uncertain significance (Mar 27, 2023)
10-68288551-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-68288596-A-C		not specified	Uncertain significance (Jan 07, 2022)
10-68288632-G-A		not specified	Uncertain significance (Nov 12, 2021)
10-68288953-G-A		not specified	Uncertain significance (Feb 28, 2023)
10-68288973-T-A		not specified	Uncertain significance (Feb 27, 2024)
10-68292037-G-T		not specified	Uncertain significance (Jul 11, 2023)
10-68292153-C-G		not specified	Uncertain significance (Feb 13, 2024)
10-68296284-C-G		not specified	Uncertain significance (May 11, 2022)
10-68306775-A-G		not specified	Uncertain significance (Mar 28, 2023)
10-68306795-C-A		not specified	Uncertain significance (Mar 31, 2023)
10-68306826-T-G		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBLD	protein_coding	protein_coding	ENST00000358769	9	50390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.34e-11	0.0381	125535	1	211	125747	0.000843

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.353	150	163	0.922	0.00000860	1877
Missense in Polyphen		42	50.945	0.82442		624
Synonymous	0.865	53	61.6	0.860	0.00000359	580
Loss of Function	-0.143	16	15.4	1.04	8.36e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0102	0.0102
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000761	0.000761
South Asian	0.000242	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.938
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.177
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.825

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbld1

Gene ontology

• Biological process: biosynthetic process;negative regulation of epithelial cell migration;negative regulation of epithelial to mesenchymal transition;maintenance of gastrointestinal epithelium;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of epithelial cell proliferation;negative regulation of SMAD protein signal transduction;negative regulation of pathway-restricted SMAD protein phosphorylation
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: molecular_function;protein binding;isomerase activity;identical protein binding