RFX7

regulatory factor X7, the group of Regulatory factor X family

Basic information

Region (hg38): 15:56087280-56245082

Previous symbols: [ "RFXDC2" ]

Links

ENSG00000181827 ∙ NCBI:64864 ∙ OMIM:612660 ∙ HGNC:25777 ∙ Uniprot:Q2KHR2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	33658631; 36334883

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RFX7 gene.

• Intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFX7 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	2	5
missense	1	1	114	32	2	150
nonsense		1	5			6
start loss						0
frameshift	1	4	4			9
inframe indel			1	2		3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		3	4
Total	2	6	125	37	7

Highest pathogenic variant AF is 0.00000657

Variants in RFX7

This is a list of pathogenic ClinVar variants found in the RFX7 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-56093369-A-C		RFX7-related disorder	Uncertain significance (Apr 20, 2023)
15-56093380-T-C			Uncertain significance (Feb 06, 2024)
15-56093460-A-C		RFX7-related disorder	Uncertain significance (Jul 05, 2024)
15-56093471-T-G			Likely benign (May 01, 2025)
15-56093499-C-G			Uncertain significance (Oct 16, 2024)
15-56093544-T-C		Inborn genetic diseases	Likely benign (Dec 08, 2023)
15-56093547-A-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2024)
15-56093577-A-G		Inborn genetic diseases	Likely benign (Nov 13, 2023)
15-56093589-A-T		Inborn genetic diseases	Uncertain significance (Jan 04, 2025)
15-56093639-C-G			Uncertain significance (Jul 05, 2022)
15-56093653-A-T			Uncertain significance (Aug 15, 2024)
15-56093661-C-A		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
15-56093661-C-G		Inborn genetic diseases	Uncertain significance (Aug 17, 2022)
15-56093682-G-C		Inborn genetic diseases	Uncertain significance (Aug 12, 2024)
15-56093688-T-C		Inborn genetic diseases	Likely benign (Mar 06, 2023)
15-56093706-T-C		Inborn genetic diseases	Uncertain significance (Aug 05, 2024)
15-56093712-A-G		Inborn genetic diseases	Uncertain significance (Jul 11, 2023)
15-56093754-T-G		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
15-56093757-C-T		Inborn genetic diseases	Likely benign (Aug 04, 2021)
15-56093786-TG-T			Uncertain significance (Jun 20, 2019)
15-56093813-G-T		Inborn genetic diseases	Uncertain significance (Oct 08, 2024)
15-56093827-T-C		Inborn genetic diseases	Uncertain significance (Mar 25, 2024)
15-56093857-T-C		not specified	Uncertain significance (Apr 10, 2025)
15-56093862-G-A			Uncertain significance (Mar 12, 2025)
15-56093877-G-A			Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFX7	protein_coding	protein_coding	ENST00000423270	9	156006

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.88e-7	124622	0	7	124629	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	637	761	0.837	0.0000388	9587
Missense in Polyphen		201	328.1	0.61262		4112
Synonymous	-0.252	280	275	1.02	0.0000143	2908
Loss of Function	6.13	2	47.6	0.0420	0.00000234	601

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000189	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000354
Middle Eastern	0.000189	0.000167
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Haploinsufficiency Scores

• pHI: 0.765
• hipred: Y
• hipred_score: 0.644
• ghis: 0.648

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.488

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rfx7
• 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); vision/eye phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• 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 factor activity