NXNL1

nucleoredoxin like 1, the group of Nucleoredoxin family

Basic information

Region (hg38): 19:17455425-17460926

Previous symbols: [ "TXNL6" ]

Links

ENSG00000171773 ∙ NCBI:115861 ∙ OMIM:608791 ∙ HGNC:25179 ∙ Uniprot:Q96CM4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Leber congenital amaurosis (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NXNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXNL1 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
missense			26	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	26	5	0

Variants in NXNL1

This is a list of pathogenic ClinVar variants found in the NXNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17455645-G-T		NXNL1-related disorder	Likely benign (Feb 22, 2019)
19-17455652-A-G		not specified	Uncertain significance (Oct 02, 2023)
19-17455668-G-C		NXNL1-related disorder	Likely benign (May 15, 2022)
19-17455685-C-G		not specified	Uncertain significance (Sep 29, 2022)
19-17455721-C-CCACGCGGTACTTGTGGCGGCGCAGG		NXNL1-related disorder	Likely benign (Apr 05, 2023)
19-17455730-A-G		not specified	Uncertain significance (Oct 22, 2021)
19-17455753-G-A			Likely benign (Jul 01, 2023)
19-17455765-G-A		not specified	Uncertain significance (Dec 06, 2023)
19-17455795-T-C		not specified	Uncertain significance (Oct 17, 2023)
19-17455814-C-T		not specified	Uncertain significance (Feb 01, 2025)
19-17455853-C-G		not specified	Uncertain significance (Nov 08, 2024)
19-17455869-G-T		not specified	Uncertain significance (Feb 16, 2023)
19-17455871-C-T		not specified	Uncertain significance (Jul 26, 2022)
19-17455880-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-17455882-C-G		not specified	Uncertain significance (Mar 31, 2023)
19-17455911-C-A		NXNL1-related disorder	Likely benign (Sep 20, 2019)
19-17455916-C-A		not specified	Uncertain significance (Jul 20, 2021)
19-17455933-T-C		not specified	Uncertain significance (Feb 06, 2023)
19-17455937-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-17455963-C-T		NXNL1-related disorder	Likely benign (Mar 01, 2019)
19-17460537-T-G			Likely benign (May 01, 2024)
19-17460565-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-17460595-T-C			Uncertain significance (May 26, 2021)
19-17460597-G-C			Likely benign (Apr 01, 2024)
19-17460626-A-G		not specified	Likely benign (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXNL1	protein_coding	protein_coding	ENST00000301944	2	5530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0119	0.658	125621	0	39	125660	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.191	125	131	0.953	0.00000760	1341
Missense in Polyphen		34	36.313	0.93631		383
Synonymous	-0.589	65	59.2	1.10	0.00000341	441
Loss of Function	0.483	3	4.05	0.741	1.73e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000236	0.000236
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000628	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.0000455	0.0000440
Middle Eastern	0.000628	0.000598
South Asian	0.000364	0.000359
Other	0.000353	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cone cell viability, slowing down cone degeneration, does not seem to play a role in degenerating rods. {ECO:0000250}.

Recessive Scores

• pRec: 0.159

Haploinsufficiency Scores

• pHI: 0.229
• hipred: N
• hipred_score: 0.340

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxnl1
• Phenotype: hematopoietic system 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); vision/eye phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell redox homeostasis;photoreceptor cell maintenance
• Cellular component: nuclear outer membrane