PHF7

PHD finger protein 7, the group of PHD finger proteins

Basic information

Region (hg38): 3:52410660-52423641

Links

ENSG00000010318 ∙ NCBI:51533 ∙ OMIM:620057 ∙ HGNC:18458 ∙ Uniprot:Q9BWX1 ∙ 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 PHF7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF7 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					3	3
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	21	1	3

Variants in PHF7

This is a list of pathogenic ClinVar variants found in the PHF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52414000-T-C		not specified	Uncertain significance (Mar 23, 2022)
3-52414022-C-G		not specified	Uncertain significance (Jun 22, 2023)
3-52414562-A-G		not specified	Uncertain significance (Nov 27, 2024)
3-52414570-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-52414586-T-G		not specified	Uncertain significance (Nov 20, 2024)
3-52419875-G-C		not specified	Uncertain significance (Sep 24, 2024)
3-52419924-C-T		not specified	Uncertain significance (Feb 01, 2025)
3-52420329-A-G		not specified	Uncertain significance (Jul 16, 2024)
3-52420344-A-G		not specified	Uncertain significance (Nov 15, 2024)
3-52420922-C-T		not specified	Uncertain significance (Mar 27, 2023)
3-52420941-A-G		not specified	Uncertain significance (Jun 18, 2021)
3-52420944-A-T		not specified	Uncertain significance (Jan 16, 2025)
3-52421040-T-C		not specified	Uncertain significance (Dec 07, 2024)
3-52421648-A-G		not specified	Uncertain significance (Dec 10, 2024)
3-52421657-C-T		Progressive sensorineural hearing impairment	Uncertain significance (Sep 03, 2016)
3-52422265-T-C		not specified	Uncertain significance (Jul 05, 2023)
3-52422763-G-T		not specified	Uncertain significance (Oct 27, 2022)
3-52422792-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-52422811-G-T		not specified	Uncertain significance (Aug 16, 2021)
3-52422817-C-T			Benign (Dec 31, 2019)
3-52422820-C-T			Benign (Dec 31, 2019)
3-52422872-G-T		not specified	Likely benign (Feb 23, 2023)
3-52423087-C-CCA		PHF7-related disorder	Benign (Dec 29, 2019)
3-52423094-A-T		not specified	Uncertain significance (Jan 22, 2024)
3-52423096-A-C		not specified	Uncertain significance (Mar 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF7	protein_coding	protein_coding	ENST00000327906	10	12985

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00108	0.997	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	158	204	0.776	0.0000103	2534
Missense in Polyphen		58	89.904	0.64513		1087
Synonymous	-0.907	81	71.3	1.14	0.00000369	642
Loss of Function	2.70	9	23.0	0.392	0.00000110	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000218	0.000217
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermatogenesis.

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• loftool: 0.225
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0942
• hipred: N
• hipred_score: 0.233
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf7

Gene ontology

• Cellular component: nucleus;nucleoplasm;Golgi apparatus;cytosol;plasma membrane;nuclear speck
• Molecular function: protein binding;metal ion binding