PPHLN1

periphilin 1

Basic information

Region (hg38): 12:42238446-42459715

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.

• Inborn genetic diseases (10 variants)

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.

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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in PPHLN1

This is a list of pathogenic ClinVar variants found in the PPHLN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-42313743-C-G		not specified	Uncertain significance (Oct 06, 2021)
12-42313754-T-C		not specified	Uncertain significance (May 03, 2023)
12-42317880-A-T		not specified	Uncertain significance (Sep 20, 2023)
12-42335973-G-C		not specified	Uncertain significance (Oct 14, 2023)
12-42355163-T-A		not specified	Uncertain significance (Feb 16, 2023)
12-42355191-G-A		not specified	Uncertain significance (Aug 22, 2023)
12-42374867-A-G		not specified	Uncertain significance (Mar 27, 2023)
12-42374895-T-C		not specified	Uncertain significance (Jan 04, 2024)
12-42374918-G-C		not specified	Uncertain significance (Nov 15, 2021)
12-42374921-C-G		not specified	Uncertain significance (Feb 10, 2023)
12-42384949-G-A		not specified	Uncertain significance (Dec 20, 2022)
12-42384954-G-C		not specified	Uncertain significance (May 15, 2023)
12-42387485-A-T		not specified	Uncertain significance (Dec 21, 2023)
12-42387531-C-T		not specified	Uncertain significance (Apr 11, 2023)
12-42393600-A-G		not specified	Uncertain significance (Jul 09, 2021)
12-42393655-A-G		not specified	Uncertain significance (Dec 22, 2023)
12-42393656-T-G		not specified	Uncertain significance (Dec 28, 2023)
12-42398993-A-C		not specified	Uncertain significance (Sep 20, 2023)
12-42441322-G-A		not specified	Uncertain significance (Mar 31, 2022)
12-42459195-C-T		Epilepsy, progressive myoclonic, 1B	Uncertain significance (Jun 14, 2016)
12-42459213-CTT-C		Epilepsy, progressive myoclonic, 1B	Uncertain significance (Jun 14, 2016)
12-42459256-GT-G		Epilepsy, progressive myoclonic, 1B	Uncertain significance (Jun 14, 2016)
12-42459548-A-G			Benign (Jun 14, 2018)
12-42459667-C-T		Epilepsy, progressive myoclonic, 1B	Uncertain significance (Jun 14, 2016)

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