PHF20L1

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

Basic information

Region (hg38): 8:132775358-132848807

Links

ENSG00000129292NCBI:51105OMIM:620050HGNC:24280Uniprot:A8MW92AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
74
clinvar
1
clinvar
75
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 74 1 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PHF20L1protein_codingprotein_codingENST00000395386 2073435
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000496125727091257360.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.854185380.7760.00002786726
Missense in Polyphen109194.080.561622423
Synonymous-0.09691851831.010.000009621830
Loss of Function6.33556.30.08890.00000310694

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003630.0000352
Middle Eastern0.000.00
South Asian0.0001340.000131
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Phf20l1
Phenotype

Gene ontology

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