NXNL2

nucleoredoxin like 2, the group of Nucleoredoxin family

Basic information

Region (hg38): 9:88534033-88584274

Previous symbols: [ "C9orf121" ]

Links

ENSG00000130045 ∙ NCBI:158046 ∙ OMIM:615299 ∙ HGNC:30482 ∙ Uniprot:Q5VZ03 ∙ 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 NXNL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXNL2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in NXNL2

This is a list of pathogenic ClinVar variants found in the NXNL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-88535457-G-C		not specified	Uncertain significance (Feb 16, 2023)
9-88535489-G-A		not specified	Uncertain significance (Oct 20, 2024)
9-88535495-G-A		not specified	Uncertain significance (Sep 14, 2023)
9-88535497-G-C		not specified	Uncertain significance (Nov 12, 2021)
9-88535533-C-G		not specified	Uncertain significance (Feb 28, 2023)
9-88535571-C-A		not specified	Likely benign (Aug 02, 2023)
9-88535673-T-C		not specified	Uncertain significance (Nov 10, 2024)
9-88535682-T-A		not specified	Uncertain significance (Aug 22, 2023)
9-88535684-C-G		not specified	Uncertain significance (Nov 18, 2022)
9-88535688-A-T		not specified	Uncertain significance (Apr 17, 2024)
9-88535727-C-G		not specified	Uncertain significance (Feb 22, 2024)
9-88544426-T-C		not specified	Uncertain significance (Jan 04, 2024)
9-88544435-A-G		not specified	Uncertain significance (Jan 17, 2025)
9-88544465-G-A		not specified	Uncertain significance (Aug 04, 2021)
9-88544465-G-T		not specified	Uncertain significance (Oct 13, 2023)
9-88544488-T-A		not specified	Uncertain significance (Oct 29, 2024)
9-88544491-G-A		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXNL2	protein_coding	protein_coding	ENST00000375854	2	49174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.677	0.304	124304	0	11	124315	0.0000442

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.167	98	93.5	1.05	0.00000472	994
Missense in Polyphen		36	30.461	1.1819		325
Synonymous	-0.733	50	43.8	1.14	0.00000235	329
Loss of Function	1.78	0	3.69	0.00	1.57e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000419	0.000374
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000284	0.0000267
Middle Eastern	0.00	0.00
South Asian	0.0000660	0.0000655
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the maintenance of both the function and the viability of sensory neurons, including photoreceptors and olfactory neurons. {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.316
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.429
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.437

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxnl2
• 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; respiratory system phenotype; craniofacial phenotype; growth/size/body region phenotype; taste/olfaction phenotype

Gene ontology

• Biological process: visual perception;sensory perception of smell;photoreceptor cell maintenance