PCID2

PCI domain containing 2, the group of Transcription and export complex 2

Basic information

Region (hg38): 13:113177535-113208715

Links

ENSG00000126226 ∙ NCBI:55795 ∙ OMIM:613713 ∙ HGNC:25653 ∙ Uniprot:Q5JVF3 ∙ 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 PCID2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCID2 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					1	1
non coding						0
Total	0	0	8	1	1

Variants in PCID2

This is a list of pathogenic ClinVar variants found in the PCID2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113178208-G-A		not specified	Uncertain significance (May 09, 2024)
13-113178291-C-T			Benign (Dec 31, 2019)
13-113180020-G-T		not specified	Likely benign (Sep 12, 2023)
13-113180162-C-T		not specified	Uncertain significance (Jan 02, 2024)
13-113181168-T-C		not specified	Uncertain significance (Dec 27, 2022)
13-113181188-G-C		not specified	Uncertain significance (Jun 06, 2023)
13-113181222-A-C		not specified	Uncertain significance (Apr 19, 2024)
13-113184358-C-T		not specified	Uncertain significance (Jun 22, 2021)
13-113190934-C-A			Benign (May 14, 2018)
13-113196209-C-T		not specified	Uncertain significance (Sep 22, 2022)
13-113196211-C-T		not specified	Uncertain significance (Sep 26, 2023)
13-113197196-C-T		not specified	Uncertain significance (Oct 05, 2023)
13-113200510-C-T		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCID2	protein_coding	protein_coding	ENST00000246505	14	31139

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-13	0.343	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	186	256	0.726	0.0000142	2993
Missense in Polyphen		33	53.917	0.61205		649
Synonymous	0.398	96	101	0.950	0.00000634	822
Loss of Function	1.22	23	30.2	0.761	0.00000162	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000345	0.000343
Middle Eastern	0.000163	0.000163
South Asian	0.000197	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for B-cell survival through the regulation of the expression of cell-cycle checkpoint MAD2L1 protein during B cell differentiation (By similarity). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export- competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. Binds and stabilizes BRCA2 and is thus involved in the control of R-loop- associated DNA damage and transcription-associated genomic instability. R-loop accumulation does not increase in PCID2- depleted cells. {ECO:0000250, ECO:0000269|PubMed:22307388, ECO:0000269|PubMed:24896180}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.262
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.517
• hipred: Y
• hipred_score: 0.721
• ghis: 0.665

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcid2
• Phenotype: immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery;transcription elongation from RNA polymerase II promoter;poly(A)+ mRNA export from nucleus;negative regulation of apoptotic process;regulation of mRNA stability;positive regulation of B cell differentiation;positive regulation of transcription, DNA-templated;spleen development;nuclear retention of pre-mRNA at the site of transcription;positive regulation of mitotic cell cycle spindle assembly checkpoint;negative regulation of cysteine-type endopeptidase activity
• Cellular component: cellular_component;transcriptionally active chromatin;transcription export complex 2
• Molecular function: double-stranded DNA binding;RNA binding;protein binding