PCNX4

pecanex 4

Basic information

Region (hg38): 14:60091910-60169133

Previous symbols: [ "C14orf135", "PCNXL4" ]

Links

ENSG00000126773 ∙ NCBI:64430 ∙ ∙ HGNC:20349 ∙ Uniprot:Q63HM2 ∙ 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 PCNX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNX4 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			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	0

Variants in PCNX4

This is a list of pathogenic ClinVar variants found in the PCNX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-60115134-C-T		not specified	Uncertain significance (Aug 02, 2021)
14-60115299-C-A		not specified	Uncertain significance (Oct 06, 2021)
14-60115720-A-G			Likely benign (Sep 01, 2022)
14-60118389-G-A		not specified	Uncertain significance (Jul 26, 2021)
14-60118516-C-G		not specified	Uncertain significance (Sep 27, 2021)
14-60121235-A-G		not specified	Uncertain significance (Jul 15, 2021)
14-60124427-C-G		not specified	Uncertain significance (Sep 27, 2021)
14-60124899-G-A		not specified	Uncertain significance (Jul 13, 2021)
14-60125690-T-A		not specified	Uncertain significance (Jul 20, 2021)
14-60125773-A-G			Likely benign (Jan 01, 2023)
14-60149363-T-C		not specified	Uncertain significance (Mar 31, 2024)
14-60149513-C-T		not specified	Uncertain significance (Sep 14, 2021)
14-60149514-G-A		not specified	Uncertain significance (Dec 14, 2023)
14-60149522-C-T		not specified	Uncertain significance (Dec 21, 2022)
14-60149556-T-C		not specified	Uncertain significance (Oct 17, 2023)
14-60150075-T-G		not specified	Uncertain significance (Dec 21, 2022)
14-60150084-A-G		not specified	Uncertain significance (Jul 20, 2021)
14-60150088-A-G		not specified	Uncertain significance (Jan 02, 2024)
14-60150172-G-A		not specified	Uncertain significance (Apr 11, 2023)
14-60150179-A-T		not specified	Uncertain significance (Mar 29, 2023)
14-60152940-C-T		not specified	Uncertain significance (May 11, 2022)
14-60152941-G-A		not specified	Uncertain significance (Jul 09, 2021)
14-60153037-C-T		not specified	Uncertain significance (Jul 06, 2021)
14-60153070-A-T		not specified	Uncertain significance (Apr 12, 2022)
14-60153075-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCNX4	protein_coding	protein_coding	ENST00000317623	9	77223

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-22	0.00254	125332	0	276	125608	0.00110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	541	477	1.13	0.0000235	6097
Missense in Polyphen		127	110.8	1.1462		1363
Synonymous	-1.91	200	169	1.19	0.00000825	1818
Loss of Function	0.382	35	37.5	0.933	0.00000182	517

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00290	0.00282
Ashkenazi Jewish	0.00	0.00
East Asian	0.00172	0.00131
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.00125	0.00123
Middle Eastern	0.00172	0.00131
South Asian	0.00126	0.00121
Other	0.00103	0.000979

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0860

Haploinsufficiency Scores

• pHI: 0.0627
• hipred: N
• hipred_score: 0.177
• ghis: 0.539

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pcnx4

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding