NFXL1

nuclear transcription factor, X-box binding like 1, the group of Ring finger proteins

Basic information

Region (hg38): 4:47847233-47914667

Links

ENSG00000170448 ∙ NCBI:152518 ∙ ∙ HGNC:18726 ∙ Uniprot:Q6ZNB6 ∙ 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 NFXL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFXL1 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						0
missense			68			68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	0	0

Variants in NFXL1

This is a list of pathogenic ClinVar variants found in the NFXL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-47848180-T-C		NFXL1-related disorder	Benign (Mar 21, 2019)
4-47848276-C-T		not specified	Uncertain significance (Jul 14, 2021)
4-47848299-C-T		not specified	Uncertain significance (Jun 10, 2024)
4-47851138-G-C		not specified	Uncertain significance (Nov 10, 2021)
4-47851140-T-G		not specified	Uncertain significance (May 13, 2024)
4-47851148-T-A		not specified	Uncertain significance (Jun 17, 2024)
4-47851881-T-C		not specified	Uncertain significance (Nov 07, 2024)
4-47851921-G-A		not specified	Uncertain significance (May 23, 2023)
4-47855088-G-C		not specified	Uncertain significance (Jan 22, 2024)
4-47855099-T-C		not specified	Uncertain significance (Jan 05, 2022)
4-47855160-G-A		not specified	Uncertain significance (Aug 22, 2023)
4-47862898-T-A		not specified	Uncertain significance (Nov 07, 2022)
4-47862904-G-C		NFXL1-related disorder	Benign (Feb 21, 2019)
4-47875128-T-C		not specified	Uncertain significance (Mar 08, 2025)
4-47875191-G-A		not specified	Uncertain significance (Jul 27, 2024)
4-47875214-C-T		not specified	Uncertain significance (Mar 28, 2024)
4-47875226-G-A		not specified	Uncertain significance (Dec 07, 2021)
4-47875296-G-C		NFXL1-related disorder	Benign (Apr 26, 2019)
4-47878664-A-G		not specified	Uncertain significance (Jun 03, 2024)
4-47879115-T-G		not specified	Uncertain significance (Aug 15, 2023)
4-47884356-G-C		not specified	Uncertain significance (Feb 22, 2025)
4-47884371-G-A		not specified	Uncertain significance (Mar 15, 2024)
4-47884401-G-A		not specified	Uncertain significance (Mar 01, 2023)
4-47884412-T-C		not specified	Uncertain significance (Jun 30, 2023)
4-47884419-A-G		not specified	Uncertain significance (Mar 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFXL1	protein_coding	protein_coding	ENST00000507489	22	67397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000124	1.00	125690	0	57	125747	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	399	485	0.822	0.0000243	5939
Missense in Polyphen		92	162.12	0.5675		1844
Synonymous	0.488	148	156	0.950	0.00000744	1642
Loss of Function	4.51	19	55.1	0.345	0.00000312	685

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000638	0.000624
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000268	0.000264
Middle Eastern	0.000165	0.000163
South Asian	0.000100	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0799

Intolerance Scores

• loftool: 0.643
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.44

Haploinsufficiency Scores

• pHI: 0.120
• hipred: Y
• hipred_score: 0.605
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.294

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfxl1
• Phenotype: growth/size/body region phenotype; limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleus;membrane;integral component of membrane
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;zinc ion binding