PCNX3

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			8 clinvar	2 clinvar		10
missense			29 clinvar	1 clinvar		30
nonsense			4 clinvar			4
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	1	48	3	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032223.4	RefSeq	NP_115599.2	35	MANE Select
ENST00000355703.4	Ensembl	ENSP00000347931.3	35	MANE Select
ENST00000913353.1	Ensembl	ENSP00000583412.1	33	Standard
ENST00000913353.2	Ensembl	ENSP00000583412.1	33	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355703
Coding exons: 35
Length: 21667
Individuals with no LoFs: 124598
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 124639
p: 0.000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.04	962	1.27e+3	0.760	0.0000857	12825
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000068	0.000065	rare
Latino/Admixed American	0.00043	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.108

Intolerance Scores

RVIS EVS: -1.42
RVIS percentile EVS: 4.12

Essentials

Essential (gene trap): N