PBDC1

polysaccharide biosynthesis domain containing 1

Basic information

Region (hg38): X:76173040-76178755

Previous symbols: [ "CXorf26" ]

Links

ENSG00000102390 ∙ NCBI:51260 ∙ ∙ HGNC:28790 ∙ Uniprot:Q9BVG4 ∙ 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 PBDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBDC1 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
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in PBDC1

This is a list of pathogenic ClinVar variants found in the PBDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-76173619-T-C		not specified	Uncertain significance (Oct 03, 2024)
X-76173619-T-G			Likely benign (Dec 01, 2022)
X-76174891-C-T		not specified	Uncertain significance (Jun 11, 2024)
X-76175556-G-T		not specified	Uncertain significance (Nov 21, 2024)
X-76176990-T-A		not specified	Uncertain significance (Nov 17, 2022)
X-76177658-G-A		not specified	Uncertain significance (Sep 27, 2021)
X-76177671-C-T			Likely benign (Dec 01, 2022)
X-76177684-A-G		not specified	Uncertain significance (May 03, 2023)
X-76177751-G-A		not specified	Uncertain significance (Jan 08, 2025)
X-76177842-C-G		not specified	Uncertain significance (Oct 07, 2024)
X-76177876-G-C		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBDC1	protein_coding	protein_coding	ENST00000373358	6	5269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.572	0.418	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.680	61	77.9	0.783	0.00000542	1531
Missense in Polyphen		13	23.559	0.5518		486
Synonymous	-1.44	35	25.7	1.36	0.00000166	408
Loss of Function	2.06	1	6.80	0.147	5.01e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0766

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.0554
• hipred: N
• hipred_score: 0.401
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbdc1

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function