PHF21B

PHD finger protein 21B, the group of PHD finger proteins

Basic information

Region (hg38): 22:44881162-45010005

Previous symbols: [ "PHF4" ]

Links

ENSG00000056487 ∙ NCBI:112885 ∙ OMIM:616727 ∙ HGNC:25161 ∙ Uniprot:Q96EK2 ∙ 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 PHF21B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF21B 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in PHF21B

This is a list of pathogenic ClinVar variants found in the PHF21B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-44883178-T-G		not specified	Uncertain significance (Aug 04, 2024)
22-44883182-C-T		not specified	Likely benign (Sep 30, 2024)
22-44883193-C-T		not specified	Uncertain significance (Oct 10, 2023)
22-44883229-G-C		not specified	Uncertain significance (Aug 04, 2021)
22-44883247-G-C		not specified	Uncertain significance (Mar 21, 2022)
22-44885439-G-A		not specified	Uncertain significance (Feb 03, 2022)
22-44885448-C-T		not specified	Uncertain significance (Jan 24, 2023)
22-44888001-G-C		not specified	Uncertain significance (Oct 06, 2022)
22-44888006-G-A		not specified	Uncertain significance (Aug 28, 2024)
22-44888034-G-A		not specified	Uncertain significance (Dec 03, 2021)
22-44888043-C-T		not specified	Uncertain significance (Oct 21, 2024)
22-44888071-G-T		not specified	Uncertain significance (Oct 29, 2024)
22-44888091-C-A		not specified	Uncertain significance (Aug 22, 2023)
22-44888107-G-C		not specified	Uncertain significance (May 02, 2024)
22-44889763-C-G		not specified	Uncertain significance (Apr 27, 2023)
22-44891311-G-A		not specified	Uncertain significance (Jul 20, 2021)
22-44891347-G-A		not specified	Uncertain significance (Jul 17, 2023)
22-44891353-C-T		not specified	Uncertain significance (Dec 03, 2024)
22-44893474-C-T		not specified	Uncertain significance (Apr 17, 2024)
22-44913898-G-A		not specified	Uncertain significance (Oct 23, 2024)
22-44913908-G-A		not specified	Uncertain significance (Sep 15, 2021)
22-44913928-G-A		not specified	Uncertain significance (Dec 20, 2021)
22-44913934-G-A		not specified	Uncertain significance (Dec 16, 2022)
22-44913977-G-A		not specified	Uncertain significance (Feb 11, 2022)
22-44913977-G-C		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF21B	protein_coding	protein_coding	ENST00000313237	13	128839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0131	125721	0	18	125739	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.642	281	313	0.898	0.0000192	3352
Missense in Polyphen		61	84.383	0.72289		922
Synonymous	-0.0747	146	145	1.01	0.00000990	1122
Loss of Function	4.21	3	26.3	0.114	0.00000137	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000682	0.0000682
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000717	0.0000703
Middle Eastern	0.000110	0.000109
South Asian	0.000131	0.000131
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.167
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.24

Haploinsufficiency Scores

• pHI: 0.109
• hipred: Y
• hipred_score: 0.710
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.794

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf21b

Gene ontology

• Molecular function: metal ion binding