ZFX

zinc finger protein X-linked, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): X:24149173-24216255

Links

ENSG00000005889 ∙ NCBI:7543 ∙ OMIM:314980 ∙ HGNC:12869 ∙ Uniprot:P17010 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked syndromic 37	XL	Cardiovascular; Endocrine; Oncologic	Among other findings, the condition can include congenital cardiac anomalies, and awareness may allow early intervention and management; Endocrine dysfunction (eg, hypogonadism, hyperparathyroidism) has been described, and early identification may enable medical management; Neoplasms have been described, and awareness may allow early detection and management	Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal	38325380

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZFX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFX 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				2	2	4
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	2

Variants in ZFX

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

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

Position	Type	Phenotype	Significance	ClinVar
X-24179192-G-T			Uncertain significance (Sep 21, 2022)
X-24179237-CTG-C		Intellectual developmental disorder, x-linked, syndromic 37	Pathogenic (Apr 02, 2024)
X-24179239-G-C		not specified	Uncertain significance (Sep 20, 2023)
X-24179316-C-A			Benign (May 02, 2018)
X-24179368-A-G		not specified	Uncertain significance (Aug 17, 2022)
X-24179428-G-A		not specified	Uncertain significance (Jul 20, 2021)
X-24179453-A-G		not specified	Uncertain significance (Jul 28, 2021)
X-24179527-A-G		not specified	Uncertain significance (Jan 31, 2022)
X-24179543-A-T		not specified	Uncertain significance (Nov 03, 2021)
X-24179570-A-G		not specified	Uncertain significance (Sep 25, 2023)
X-24179647-G-A		not specified	Uncertain significance (Apr 11, 2023)
X-24179721-CCAG-C			Uncertain significance (Oct 19, 2023)
X-24207328-G-A		Intellectual developmental disorder, x-linked, syndromic 37	Uncertain significance (Oct 10, 2024)
X-24207394-G-T			Uncertain significance (Jul 05, 2023)
X-24207759-G-A			Uncertain significance (Jun 11, 2024)
X-24207789-C-T		not specified	Uncertain significance (Mar 29, 2023)
X-24207826-A-G		not specified	Uncertain significance (May 31, 2022)
X-24208255-G-T			Likely benign (Sep 01, 2022)
X-24210271-G-GT		Intellectual developmental disorder, x-linked, syndromic 37	Pathogenic (Apr 02, 2024)
X-24210293-A-C		not specified	Uncertain significance (Mar 02, 2023)
X-24210336-GACTGTGATTAC-G			Uncertain significance (Jan 17, 2024)
X-24210487-A-C			Uncertain significance (Aug 06, 2022)
X-24210512-G-A		not specified	Uncertain significance (Jun 10, 2024)
X-24210545-T-C			Benign (Apr 16, 2018)
X-24210835-T-C		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFX	protein_coding	protein_coding	ENST00000379177	7	67083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00169	120961	0	1	120962	0.00000413

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.15	158	315	0.501	0.0000239	5437
Missense in Polyphen		50	140.25	0.3565		2569
Synonymous	-0.0804	120	119	1.01	0.0000102	1439
Loss of Function	4.00	0	18.6	0.00	0.00000133	386

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000379	0.0000379
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcriptional activator.
• Pathway: Hematopoietic Stem Cell Gene Regulation by GABP alpha-beta Complex (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• loftool: 0.0922
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.487
• hipred: Y
• hipred_score: 0.572
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfx
• Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; embryo phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: ovarian follicle development;regulation of transcription by RNA polymerase II;spermatogenesis;fertilization;post-embryonic development;multicellular organism growth;oocyte development;homeostasis of number of cells;parental behavior;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleoplasm;nucleolus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;transcription coactivator activity;metal ion binding