PHF20L1

PHD finger protein 20 like 1, the group of Tudor domain containing|PHD finger proteins

Basic information

Region (hg38): 8:132775358-132848807

Links

ENSG00000129292 ∙ NCBI:51105 ∙ OMIM:620050 ∙ HGNC:24280 ∙ Uniprot:A8MW92 ∙ 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 PHF20L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF20L1 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
missense			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	1

Variants in PHF20L1

This is a list of pathogenic ClinVar variants found in the PHF20L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-132777871-A-T		not specified	Uncertain significance (Oct 12, 2022)
8-132794471-C-T		not specified	Uncertain significance (Mar 18, 2024)
8-132794472-G-A		not specified	Uncertain significance (Jul 14, 2021)
8-132794809-A-G		not specified	Uncertain significance (Jul 26, 2022)
8-132798801-G-A		not specified	Uncertain significance (Mar 23, 2023)
8-132798828-A-G		not specified	Uncertain significance (Apr 29, 2022)
8-132803876-A-G		not specified	Uncertain significance (May 18, 2022)
8-132804003-A-G		not specified	Uncertain significance (Sep 29, 2023)
8-132804004-A-C		not specified	Uncertain significance (May 28, 2024)
8-132804667-A-G			Benign (Jul 13, 2018)
8-132814721-T-C		not specified	Uncertain significance (May 31, 2023)
8-132814838-G-A		not specified	Uncertain significance (Apr 28, 2023)
8-132816936-G-A		not specified	Uncertain significance (Dec 07, 2021)
8-132817032-T-C		not specified	Uncertain significance (Jun 07, 2023)
8-132817348-T-C		not specified	Uncertain significance (Jan 16, 2024)
8-132817416-A-G		not specified	Uncertain significance (Mar 07, 2024)
8-132824010-C-T		not specified	Uncertain significance (Nov 09, 2023)
8-132825272-A-G		not specified	Uncertain significance (Oct 22, 2021)
8-132825309-A-G		not specified	Uncertain significance (Dec 04, 2024)
8-132825369-A-T		not specified	Uncertain significance (Apr 20, 2024)
8-132832255-A-G		not specified	Uncertain significance (Oct 02, 2023)
8-132832329-C-G		not specified	Uncertain significance (Dec 09, 2023)
8-132836627-C-A		not specified	Uncertain significance (Oct 16, 2024)
8-132837800-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-132839410-C-T		not specified	Uncertain significance (Oct 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF20L1	protein_coding	protein_coding	ENST00000395386	20	73435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000496	125727	0	9	125736	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	418	538	0.776	0.0000278	6726
Missense in Polyphen		109	194.08	0.56162		2423
Synonymous	-0.0969	185	183	1.01	0.00000962	1830
Loss of Function	6.33	5	56.3	0.0889	0.00000310	694

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000363	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.476
• rvis_EVS: -1.37
• rvis_percentile_EVS: 4.43

Haploinsufficiency Scores

• pHI: 0.272
• hipred: Y
• hipred_score: 0.662
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.588

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf20l1

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: protein binding;metal ion binding