PCNX4

protein-coding

pecanex 4

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf135
PCNXL4

MANE transcript

NM_001330177.2

Inheritance

—

ClinVar variants

U:26B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr14:60,091,911-60,169,133

External References & Databases

Ensembl (ENSG00000126773)

Transcript & Mutation Effects

hg38 • Region Span ~77.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCNX4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 11

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330177.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			17 clinvar	1 clinvar		18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	26	2	0	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330177.2	RefSeq	NP_001317106.1	10	MANE Select
ENST00000406854.6	Ensembl	ENSP00000384801.1	10	MANE Select
NM_022495.5	RefSeq	NP_071940.4	9	Standard
ENST00000317623.8	Ensembl	ENSP00000317396.4	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317623
Coding exons: 9
Length: 77223
Individuals with no LoFs: 125332
Homozygous LoFs: 0
Heterozygous LoFs: 276
Defined: 125608
p: 0.00110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.04	541	477	1.13	0.0000235	6097
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.0013	0.0012	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0017	0.0013	notable
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.0013	0.0012	notable
South Asian	0.0013	0.0012	notable
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0860

Essentials

Essential (gene trap): N