PHRF1

PHD and ring finger domains 1, the group of Ring finger proteins|Protein phosphatase 1 regulatory subunits|PHD finger proteins

Basic information

Region (hg38): 11:576470-612222

Previous symbols: [ "RNF221" ]

Links

ENSG00000070047 ∙ NCBI:57661 ∙ OMIM:611780 ∙ HGNC:24351 ∙ Uniprot:Q9P1Y6 ∙ 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 PHRF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHRF1 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				6	1	7
missense			155	34	3	192
nonsense						0
start loss						0
frameshift				2		2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	155	42	4

Variants in PHRF1

This is a list of pathogenic ClinVar variants found in the PHRF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-581522-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-581559-C-T		not specified	Uncertain significance (Aug 11, 2022)
11-581597-G-A		not specified	Likely benign (Jul 12, 2023)
11-581605-T-C			Likely benign (May 01, 2023)
11-581983-G-A		not specified	Uncertain significance (Oct 03, 2022)
11-581994-G-C		not specified	Uncertain significance (Mar 04, 2024)
11-582033-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-587266-G-T		not specified	Uncertain significance (Jul 17, 2023)
11-587279-G-A		not specified	Uncertain significance (Jun 21, 2022)
11-587327-G-A		not specified	Uncertain significance (Jan 27, 2022)
11-587343-A-G		not specified	Uncertain significance (Jan 24, 2023)
11-587352-A-G		not specified	Uncertain significance (Apr 08, 2022)
11-587384-G-A		not specified	Likely benign (Sep 16, 2021)
11-587385-C-T		not specified	Uncertain significance (Apr 05, 2023)
11-587423-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-587447-A-G		not specified	Uncertain significance (Dec 20, 2023)
11-591418-T-A		not specified	Uncertain significance (Jun 06, 2023)
11-591433-T-G		not specified	Uncertain significance (Mar 04, 2024)
11-591446-T-A		not specified	Uncertain significance (Jun 28, 2022)
11-592581-C-T		not specified	Uncertain significance (Sep 13, 2023)
11-592598-G-T		not specified	Uncertain significance (Oct 04, 2022)
11-592602-C-T		not specified	Uncertain significance (Jan 03, 2022)
11-592622-G-A		not specified	Uncertain significance (May 24, 2024)
11-592661-G-A		not specified	Uncertain significance (May 30, 2023)
11-596940-T-C		not specified	Uncertain significance (Dec 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHRF1	protein_coding	protein_coding	ENST00000416188	17	35737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0565	0.943	124718	1	163	124882	0.000657

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.56	1207	1.06e+3	1.14	0.0000744	10505
Missense in Polyphen		339	329.87	1.0277		3160
Synonymous	-4.34	597	476	1.25	0.0000367	3556
Loss of Function	5.40	15	60.2	0.249	0.00000392	634

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0162	0.00817
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000563	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000266	0.000186
Middle Eastern	0.0000563	0.0000556
South Asian	0.000197	0.000163
Other	0.00123	0.000988

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.131
• rvis_EVS: -1.58
• rvis_percentile_EVS: 3.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.270
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phrf1

Gene ontology

• Biological process: transcription by RNA polymerase II;mRNA processing
• Cellular component: membrane
• Molecular function: protein domain specific binding;metal ion binding;RNA polymerase binding