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.

• not_specified (75 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000016018.5. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			74	1		75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	74	1	1

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