PCED1B

PC-esterase domain containing 1B, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 12:47079603-47236662

Previous symbols: [ "FAM113B" ]

Links

ENSG00000179715 ∙ NCBI:91523 ∙ ∙ HGNC:28255 ∙ Uniprot:Q96HM7 ∙ 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 PCED1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCED1B 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in PCED1B

This is a list of pathogenic ClinVar variants found in the PCED1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-47235073-C-A		not specified	Uncertain significance (Oct 04, 2024)
12-47235085-G-A		not specified	Uncertain significance (Oct 29, 2021)
12-47235107-A-G		not specified	Uncertain significance (Aug 07, 2024)
12-47235146-C-G		not specified	Uncertain significance (Sep 28, 2021)
12-47235253-G-A		not specified	Uncertain significance (Jan 11, 2023)
12-47235356-A-G		not specified	Uncertain significance (Apr 27, 2024)
12-47235371-A-G		not specified	Uncertain significance (Aug 12, 2022)
12-47235422-T-C		not specified	Uncertain significance (Aug 09, 2021)
12-47235436-C-T		not specified	Uncertain significance (Dec 13, 2023)
12-47235493-G-C		not specified	Uncertain significance (Nov 17, 2023)
12-47235587-G-A		not specified	Uncertain significance (Feb 01, 2023)
12-47235602-A-G		not specified	Uncertain significance (Jun 13, 2024)
12-47235779-G-A		not specified	Uncertain significance (May 17, 2023)
12-47235794-T-G		not specified	Uncertain significance (Dec 05, 2024)
12-47235800-C-T		not specified	Uncertain significance (May 26, 2022)
12-47235847-G-A		not specified	Uncertain significance (Dec 09, 2023)
12-47235896-C-T		not specified	Uncertain significance (Aug 01, 2024)
12-47235938-C-T		not specified	Uncertain significance (Oct 04, 2024)
12-47235955-A-G		not specified	Uncertain significance (Jul 14, 2024)
12-47235968-T-C		not specified	Uncertain significance (Sep 16, 2021)
12-47236010-T-A		not specified	Uncertain significance (Sep 10, 2024)
12-47236233-G-C		not specified	Uncertain significance (May 20, 2024)
12-47236237-C-A		not specified	Uncertain significance (Oct 29, 2021)
12-47236253-A-G		not specified	Uncertain significance (Mar 20, 2024)
12-47236258-G-A		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCED1B	protein_coding	protein_coding	ENST00000546455	1	157058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.926	244	288	0.847	0.0000198	2774
Missense in Polyphen		74	97.912	0.75578		1037
Synonymous	0.476	118	125	0.946	0.00000864	925
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.0951
• hipred: N
• hipred_score: 0.139
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pced1b

Gene ontology

• Molecular function: protein binding