PNN

pinin, desmosome associated protein

Basic information

Region (hg38): 14:39175183-39183220

Links

ENSG00000100941 ∙ NCBI:5411 ∙ OMIM:603154 ∙ HGNC:9162 ∙ Uniprot:Q9H307 ∙ 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 PNN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNN 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				1	1	2
missense			54		1	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	54	1	3

Variants in PNN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-39175287-T-C		not specified	Uncertain significance (Jan 20, 2023)
14-39175290-C-T		not specified	Uncertain significance (Sep 20, 2023)
14-39175364-C-T		not specified	Uncertain significance (Jul 16, 2024)
14-39176159-C-T			Benign (Dec 31, 2019)
14-39176558-C-T		not specified	Uncertain significance (Nov 09, 2024)
14-39177416-G-A		not specified	Uncertain significance (Aug 06, 2024)
14-39177596-G-A		not specified	Uncertain significance (Mar 23, 2023)
14-39177638-C-T		not specified	Uncertain significance (Dec 28, 2022)
14-39177654-A-G		not specified	Uncertain significance (Dec 09, 2024)
14-39177914-A-G		not specified	Uncertain significance (Oct 29, 2024)
14-39179145-A-C			Benign/Likely benign (Jul 01, 2023)
14-39179149-A-G		not specified	Uncertain significance (Oct 20, 2024)
14-39179228-A-C		not specified	Uncertain significance (Dec 10, 2024)
14-39179417-C-A		not specified	Uncertain significance (Mar 16, 2022)
14-39179435-A-G		not specified	Uncertain significance (Aug 02, 2021)
14-39180605-G-A		not specified	Uncertain significance (Apr 15, 2024)
14-39180657-G-T		not specified	Uncertain significance (Jun 01, 2022)
14-39180737-C-T		not specified	Uncertain significance (Feb 27, 2023)
14-39180749-G-T		not specified	Uncertain significance (Jan 23, 2024)
14-39180764-A-T		not specified	Uncertain significance (May 30, 2024)
14-39180811-G-A		not specified	Uncertain significance (Jan 03, 2024)
14-39180848-A-G		not specified	Uncertain significance (Sep 27, 2024)
14-39180869-T-C		not specified	Uncertain significance (Jan 20, 2023)
14-39180871-G-A		not specified	Uncertain significance (Jun 07, 2023)
14-39180970-G-C		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNN	protein_coding	protein_coding	ENST00000216832	9	8036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.113	0.887	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.926	344	396	0.869	0.0000214	4767
Missense in Polyphen		46	86.852	0.52964		1059
Synonymous	-1.36	148	128	1.15	0.00000625	1278
Loss of Function	4.14	9	35.7	0.252	0.00000204	426

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000275	0.000272
Finnish	0.0000978	0.0000924
European (Non-Finnish)	0.0000977	0.0000967
Middle Eastern	0.000275	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator binding to the E-box 1 core sequence of the E-cadherin promoter gene; the core-binding sequence is 5'CAGGTG-3'. Capable of reversing CTBP1-mediated transcription repression. Auxiliary component of the splicing- dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Participates in the regulation of alternative pre-mRNA splicing. Associates to spliced mRNA within 60 nt upstream of the 5'-splice sites. Component of the PSAP complex which binds RNA in a sequence-independent manner and is proposed to be recruited to the EJC prior to or during the splicing process and to regulate specific excision of introns in specific transcription subsets. Involved in the establishment and maintenance of epithelia cell- cell adhesion. Potential tumor suppressor for renal cell carcinoma. {ECO:0000269|PubMed:12051732, ECO:0000269|PubMed:14517304, ECO:0000269|PubMed:15542832, ECO:0000269|PubMed:15735603, ECO:0000269|PubMed:22388736}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.259

Intolerance Scores

• loftool: 0.559
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.78

Haploinsufficiency Scores

• pHI: 0.712
• hipred: Y
• hipred_score: 0.704
• ghis: 0.626

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pnn
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; digestive/alimentary phenotype; vision/eye phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: pnn
• Affected structure: neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: mRNA splicing, via spliceosome;cell adhesion
• Cellular component: intermediate filament;plasma membrane;cell-cell junction;membrane;nuclear speck;desmosome;exon-exon junction complex;catalytic step 2 spliceosome
• Molecular function: DNA binding;RNA binding;structural molecule activity;protein binding