RFX1

regulatory factor X1, the group of Regulatory factor X family

Basic information

Region (hg38): 19:13961530-14007039

Links

ENSG00000132005 ∙ NCBI:5989 ∙ OMIM:600006 ∙ HGNC:9982 ∙ Uniprot:P22670 ∙ 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 RFX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFX1 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					7	7
missense			54	4	4	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	54	4	11

Variants in RFX1

This is a list of pathogenic ClinVar variants found in the RFX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-13962709-G-T		not specified	Uncertain significance (Nov 22, 2024)
19-13962712-C-T		not specified	Uncertain significance (Jul 11, 2023)
19-13962719-G-T		not specified	Uncertain significance (Apr 11, 2023)
19-13962736-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-13962768-G-A		not specified	Uncertain significance (May 12, 2024)
19-13962777-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-13962853-C-T		not specified	Uncertain significance (Jan 12, 2024)
19-13962859-C-T		not specified	Uncertain significance (May 25, 2022)
19-13963013-G-T		not specified	Uncertain significance (Feb 10, 2022)
19-13963023-G-A		not specified	Uncertain significance (Nov 23, 2024)
19-13963033-T-G		not specified	Uncertain significance (Dec 03, 2021)
19-13963118-G-A			Benign (Apr 04, 2018)
19-13963151-C-T		Abnormality of neuronal migration	Benign (Oct 31, 2014)
19-13963210-C-T		not specified	Uncertain significance (Nov 23, 2024)
19-13963626-C-G		not specified	Uncertain significance (Oct 14, 2023)
19-13963655-A-T		not specified	Uncertain significance (Aug 02, 2021)
19-13963680-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-13963887-G-T		not specified	Uncertain significance (Feb 26, 2024)
19-13963921-C-G		not specified	Uncertain significance (May 26, 2024)
19-13963937-G-A		not specified	Uncertain significance (Jun 06, 2023)
19-13963975-C-T			Benign (Jun 08, 2018)
19-13965456-C-T			Benign (May 31, 2018)
19-13965494-G-A			Benign (Apr 19, 2018)
19-13965494-G-C			Benign (May 31, 2018)
19-13965539-C-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFX1	protein_coding	protein_coding	ENST00000254325	20	45502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00276	125676	0	8	125684	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.69	431	620	0.696	0.0000432	6197
Missense in Polyphen		89	202.54	0.43943		1928
Synonymous	0.623	285	299	0.954	0.0000249	2027
Loss of Function	5.50	7	48.2	0.145	0.00000225	510

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000648	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000372	0.0000352
Middle Eastern	0.0000648	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000360	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.0450
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.15

Haploinsufficiency Scores

• pHI: 0.653
• hipred: Y
• hipred_score: 0.840
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rfx1
• Phenotype: cellular 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); hearing/vestibular/ear 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)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;immune response
• Cellular component: nucleus;nucleoplasm;intracellular membrane-bounded organelle
• 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;protein binding