PCNX3

pecanex 3, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 11:65615776-65637439

Previous symbols: [ "PCNXL3" ]

Links

ENSG00000197136 ∙ NCBI:399909 ∙ OMIM:617657 ∙ HGNC:18760 ∙ Uniprot:Q9H6A9 ∙ 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 PCNX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNX3 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				2		2
missense			14	1		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	14	3	0

Variants in PCNX3

This is a list of pathogenic ClinVar variants found in the PCNX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65616897-CTG-C		Moyamoya angiopathy	Likely pathogenic (-)
11-65617648-T-A		not specified	Uncertain significance (Jul 06, 2021)
11-65618790-G-A			Likely benign (Apr 01, 2022)
11-65619830-G-A		not specified	Uncertain significance (Jun 18, 2021)
11-65619914-T-C		not specified	Uncertain significance (Jul 26, 2021)
11-65620889-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-65623629-G-A			Likely benign (Jan 01, 2023)
11-65625273-G-A		not specified	Uncertain significance (Oct 22, 2021)
11-65625482-C-T		not specified	Uncertain significance (Aug 16, 2021)
11-65625665-A-G		not specified	Uncertain significance (Oct 06, 2021)
11-65627527-G-T		not specified	Uncertain significance (Sep 01, 2021)
11-65629656-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-65634190-C-T		not specified	Uncertain significance (Oct 12, 2021)
11-65634315-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-65634346-G-A		not specified	Uncertain significance (Oct 27, 2021)
11-65635544-G-A		not specified	Uncertain significance (Aug 23, 2021)
11-65636925-A-G		not specified	Likely benign (Sep 01, 2021)
11-65636944-C-G		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCNX3	protein_coding	protein_coding	ENST00000355703	35	21667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000639	124598	0	41	124639	0.000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.04	962	1.27e+3	0.760	0.0000857	12825
Missense in Polyphen		169	392.74	0.43031		3851
Synonymous	-3.52	653	548	1.19	0.0000375	4329
Loss of Function	7.57	13	90.9	0.143	0.00000484	944

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000499	0.000495
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000200	0.000195
Middle Eastern	0.000112	0.000111
South Asian	0.0000655	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -1.42
• rvis_percentile_EVS: 4.12

Haploinsufficiency Scores

• pHI: 0.642
• hipred: Y
• hipred_score: 0.627
• ghis: 0.533

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pcnx3

Gene ontology

• Cellular component: integral component of membrane