PPHLN1

periphilin 1

Basic information

Region (hg38): 12:42238447-42459715

Links

ENSG00000134283

∙ NCBI:51535 ∙ OMIM:608150 ∙ HGNC:19369 ∙ Uniprot:Q8NEY8 ∙ 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 PPHLN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPHLN1 gene is commonly pathogenic or not. These statistics are base on trasncript: . Only rare variants are included in the table.

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			23 clinvar	1 clinvar		24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPHLN1	protein_coding	protein_coding	ENST00000395568	12	221269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.30e-8	0.984	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.762	224	258	0.867	0.0000146	2952
Missense in Polyphen		36	53.118	0.67773		715
Synonymous	0.229	88	90.8	0.969	0.00000506	869
Loss of Function	2.26	17	30.5	0.557	0.00000186	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000225	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the HUSH complex, a multiprotein complex that mediates epigenetic repression. The HUSH complex is recruited to genomic loci rich in H3K9me3 and is probably required to maintain transcriptional silencing by promoting recruitment of SETDB1, a histone methyltransferase that mediates further deposition of H3K9me3. In the HUSH complex, contributes to the maintenance of the complex at chromatin (PubMed:26022416). Acts as a transcriptional corepressor and regulates the cell cycle, probably via the HUSH complex (PubMed:15474462, PubMed:17963697). May be involved in epithelial differentiation by contributing to epidermal integrity and barrier formation (Probable). {ECO:0000269|PubMed:15474462, ECO:0000269|PubMed:17963697, ECO:0000269|PubMed:26022416, ECO:0000305|PubMed:12853457}.;

Recessive Scores

pRec: 0.100

Intolerance Scores

loftool: 0.0364
rvis_EVS: -0.25
rvis_percentile_EVS: 36.07

Haploinsufficiency Scores

pHI: 0.101
hipred: Y
hipred_score: 0.607
ghis: 0.531

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.768

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pphln1
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);

Gene ontology

Biological process: keratinization;negative regulation of transcription, DNA-templated
Cellular component: nucleoplasm;chromosome;Golgi apparatus;cytosol
Molecular function: RNA binding;protein binding