RFX4

regulatory factor X4, the group of Regulatory factor X family

Basic information

Region (hg38): 12:106583003-106762803

Links

ENSG00000111783 ∙ NCBI:5992 ∙ OMIM:603958 ∙ HGNC:9985 ∙ Uniprot:Q33E94 ∙ 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 RFX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFX4 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				1	1	2
missense			33	1	2	36
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding					1	1
Total	0	0	35	3	4

Variants in RFX4

This is a list of pathogenic ClinVar variants found in the RFX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-106601313-G-A		not specified	Uncertain significance (May 28, 2024)
12-106601320-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-106601331-C-G			Benign (Jun 08, 2018)
12-106601349-A-G			Benign (Jun 08, 2018)
12-106608780-C-CTT		RFX4-related disorder	Likely benign (Oct 19, 2020)
12-106608838-C-A		not specified	Uncertain significance (Nov 12, 2021)
12-106639356-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-106639364-C-T		not specified	Uncertain significance (Jan 07, 2022)
12-106639376-C-T			Uncertain significance (-)
12-106654233-AG-A			Uncertain significance (May 27, 2022)
12-106654271-C-T			Uncertain significance (Apr 01, 2023)
12-106654280-C-T		not specified	Uncertain significance (Aug 08, 2022)
12-106654290-A-G			Uncertain significance (Sep 20, 2022)
12-106682041-C-T			Uncertain significance (Mar 17, 2023)
12-106686973-C-T		not specified	Uncertain significance (Aug 31, 2022)
12-106687000-C-T		not specified	Uncertain significance (Jul 19, 2023)
12-106687017-C-T		not specified	Uncertain significance (Jun 11, 2021)
12-106689354-A-C		not specified	Uncertain significance (Jan 10, 2023)
12-106696373-G-A		not specified	Uncertain significance (Dec 22, 2023)
12-106696400-A-G		not specified	Uncertain significance (Nov 17, 2023)
12-106696406-G-A		not specified	Uncertain significance (Sep 29, 2022)
12-106711482-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-106715434-C-T		not specified	Uncertain significance (Dec 26, 2023)
12-106715499-A-G		not specified	Uncertain significance (Apr 17, 2024)
12-106715515-G-A		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFX4	protein_coding	protein_coding	ENST00000357881	18	179897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000557	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	301	431	0.698	0.0000245	4862
Missense in Polyphen		64	128.78	0.49696		1459
Synonymous	0.647	157	168	0.936	0.0000104	1443
Loss of Function	5.77	2	42.7	0.0468	0.00000226	473

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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: Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development. {ECO:0000250|UniProtKB:Q7TNK1}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.0419
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.93

Haploinsufficiency Scores

• pHI: 0.466
• hipred: Y
• hipred_score: 0.837
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.845

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rfx4
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: rfx4
• Affected structure: roof plate
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;telencephalon development;negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning;positive regulation of transcription by RNA polymerase II;cilium assembly;regulation of protein processing
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding