PCED1A

PC-esterase domain containing 1A

Basic information

Region (hg38): 20:2835313-2841190

Previous symbols: [ "C20orf81", "FAM113A" ]

Links

ENSG00000132635 ∙ NCBI:64773 ∙ ∙ HGNC:16212 ∙ Uniprot:Q9H1Q7 ∙ 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 PCED1A gene.

• Inborn genetic diseases (18 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCED1A 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	18	1	1

Variants in PCED1A

This is a list of pathogenic ClinVar variants found in the PCED1A region.

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

Position	Type	Phenotype	Significance	ClinVar
20-2835502-T-C		not specified	Uncertain significance (Feb 11, 2022)
20-2835545-G-A		not specified	Uncertain significance (Jan 20, 2023)
20-2835559-C-T		not specified	Uncertain significance (Nov 09, 2023)
20-2835602-G-A		not specified	Uncertain significance (Dec 27, 2023)
20-2835635-G-A		not specified	Uncertain significance (Dec 21, 2022)
20-2836048-G-A		not specified	Uncertain significance (Oct 29, 2021)
20-2836092-T-C		not specified	Uncertain significance (Dec 12, 2022)
20-2836098-G-T		not specified	Uncertain significance (Oct 26, 2021)
20-2836144-G-C		not specified	Uncertain significance (Sep 16, 2021)
20-2836164-G-A		not specified	Uncertain significance (Feb 16, 2023)
20-2836225-G-A		not specified	Uncertain significance (Nov 02, 2023)
20-2836263-T-C		not specified	Uncertain significance (Oct 27, 2022)
20-2836283-A-T		not specified	Uncertain significance (Feb 17, 2024)
20-2836296-C-G		not specified	Uncertain significance (Mar 01, 2024)
20-2838240-T-C		not specified	Uncertain significance (Sep 01, 2021)
20-2838285-G-A			Likely benign (Apr 01, 2022)
20-2838349-G-A		not specified	Uncertain significance (Dec 21, 2022)
20-2838403-G-A		not specified	Uncertain significance (Dec 14, 2021)
20-2838448-C-T		not specified	Uncertain significance (May 03, 2023)
20-2838450-C-T		not specified	Uncertain significance (Jun 28, 2022)
20-2838454-G-A		not specified	Uncertain significance (Jun 24, 2022)
20-2838702-C-T		not specified	Uncertain significance (Jun 29, 2022)
20-2838905-G-T		not specified	Uncertain significance (Jul 06, 2021)
20-2838943-C-T		not specified	Uncertain significance (Dec 18, 2023)
20-2839241-A-T		not specified	Uncertain significance (Jan 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCED1A	protein_coding	protein_coding	ENST00000360652	7	5877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0924	0.906	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.689	241	273	0.883	0.0000180	2934
Missense in Polyphen		55	94.241	0.58361		1085
Synonymous	-0.466	119	113	1.06	0.00000684	948
Loss of Function	2.77	5	17.5	0.286	8.40e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.000323	0.000277
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.257
• hipred: N
• hipred_score: 0.348
• ghis: 0.541

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: Pced1a
• Phenotype: immune system phenotype; hematopoietic system phenotype; skeleton phenotype

Gene ontology

• Molecular function: protein binding