PCNX2

pecanex 2

Basic information

Region (hg38): 1:232983434-233295725

Previous symbols: [ "PCNXL2" ]

Links

ENSG00000135749 ∙ NCBI:80003 ∙ OMIM:617656 ∙ HGNC:8736 ∙ Uniprot:A6NKB5 ∙ 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 PCNX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNX2 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				5	2	7
missense			24	3		27
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	2	4
non coding					2	2
Total	0	0	25	8	4

Variants in PCNX2

This is a list of pathogenic ClinVar variants found in the PCNX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-232984441-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-232984475-G-A			Benign (May 17, 2018)
1-232986152-T-A			Benign (Mar 29, 2018)
1-232986206-G-A			Likely benign (Apr 04, 2018)
1-232986293-G-T			Likely benign (May 01, 2022)
1-232998405-A-T		not specified	Uncertain significance (Sep 14, 2021)
1-233000385-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-233017003-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCT			Benign (Jan 05, 2024)
1-233025206-G-A			Likely benign (Apr 04, 2018)
1-233025234-A-G		not specified	Uncertain significance (Aug 17, 2021)
1-233054371-G-A			Likely benign (Dec 01, 2022)
1-233057240-CTT-C		not specified	Uncertain significance (Sep 11, 2015)
1-233090143-T-C		not specified	Uncertain significance (Jul 06, 2021)
1-233095873-A-G			Benign (Apr 04, 2018)
1-233139847-G-A		not specified	Uncertain significance (Sep 11, 2015)
1-233161321-C-A		not specified	Uncertain significance (Oct 22, 2021)
1-233161361-C-T			Uncertain significance (Dec 01, 2022)
1-233179093-C-T		not specified	Uncertain significance (Aug 28, 2021)
1-233179171-G-T		not specified	Uncertain significance (Aug 02, 2021)
1-233198986-C-T		not specified	Likely benign (Nov 12, 2021)
1-233200199-T-C			Likely benign (May 01, 2022)
1-233200215-T-G		not specified	Uncertain significance (Oct 22, 2021)
1-233227227-G-T			Benign (Jan 02, 2018)
1-233227341-A-G		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCNX2	protein_coding	protein_coding	ENST00000258229	34	312279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-23	1.00	124635	0	216	124851	0.000865

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	1065	1.18e+3	0.901	0.0000677	13928
Missense in Polyphen		209	290.46	0.71954		3420
Synonymous	-0.0872	494	492	1.00	0.0000318	4215
Loss of Function	4.23	54	99.5	0.543	0.00000537	1127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00297	0.00295
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.000681	0.000667
Finnish	0.000572	0.000557
European (Non-Finnish)	0.000718	0.000681
Middle Eastern	0.000681	0.000667
South Asian	0.000771	0.000752
Other	0.00151	0.00148

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in tumorigenesis of colorectal carcinomas with high microsatellite instability (MSI-H). {ECO:0000269|PubMed:12140758, ECO:0000269|PubMed:14507650}.

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.7

Haploinsufficiency Scores

• pHI: 0.0995
• hipred: N
• hipred_score: 0.414
• ghis: 0.552

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pcnx2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function