PBDC1

protein-coding

polysaccharide biosynthesis domain containing 1

Gene summary

Predicted to enable protein folding chaperone. Predicted to be involved in 'de novo' cotranslational protein folding. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CXorf26

MANE transcript

NM_016500.5

Inheritance

—

ClinVar variants

U:41B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chrX:76,173,040-76,178,755

External References & Databases

Ensembl (ENSG00000102390)

Transcript & Mutation Effects

hg38 • Region Span ~5.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PBDC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 16

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016500.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	1 clinvar		6
missense			24 clinvar	2 clinvar		26
nonsense			1 clinvar			1
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	41	3	0	44

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016500.5	RefSeq	NP_057584.2	6	MANE Select
ENST00000373358.8	Ensembl	ENSP00000362456.3	6	MANE Select
NM_001300888.2	RefSeq	NP_001287817.1	5	Standard
ENST00000373357.3	Ensembl	ENSP00000362455.3	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373358
Coding exons: 6
Length: 5269
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.680	61	77.9	0.783	0.00000542	1531
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0766

Intolerance Scores

RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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