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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 2 of 2.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_138454.2	NP_612463.1	2	yes	-
ENST00000301944.3	ENSP00000305631.2	2	yes	-

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.

• not_specified (43 variants)
• not_provided (6 variants)
• NXNL1-related_disorder (5 variants)

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. These statistics are base on transcript: NM_138454.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5		5
missense			43	3		46
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	9	0

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
		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

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

Gene ontology

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