PCNX2

protein-coding

pecanex 2

Gene summary

This gene contains coding mononucleotide repeats that are associated with tumors of high mcrosatellite instability (MSI-H). Defects in this gene are involved in the tumorigenesis of MSI-H colorectal carcinomas. [provided by RefSeq, Jun 2016]

Previous symbols:

PCNXL2

MANE transcript

NM_014801.4

Inheritance

—

ClinVar variants

U:50B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr1:232,983,435-233,295,725

External References & Databases

Ensembl (ENSG00000135749)

Transcript & Mutation Effects

hg38 • Region Span ~312.3 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 PCNX2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 17

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014801.4. 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	5 clinvar	4 clinvar	11
missense			39 clinvar	3 clinvar		42
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	50	8	4	62

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014801.4	RefSeq	NP_055616.3	34	MANE Select
ENST00000258229.14	Ensembl	ENSP00000258229.8	34	MANE Select
NM_001328607.3	RefSeq	NP_001315536.1	2	Standard
ENST00000344698.6	Ensembl	ENSP00000340759.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258229
Coding exons: 34
Length: 312279
Individuals with no LoFs: 124635
Homozygous LoFs: 0
Heterozygous LoFs: 216
Defined: 124851
p: 0.000865

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.21	1065	1.18e+3	0.901	0.0000677	13928
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0011	notable
Latino/Admixed American	0.0019	0.0018	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00068	0.00067	rare
Finnish	0.00057	0.00056	rare
European (Non-Finnish)	0.00072	0.00068	rare
South Asian	0.00077	0.00075	rare
Other	0.0015	0.0015	notable

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N