NXNL1

protein-coding

nucleoredoxin like 1, the group of Nucleoredoxin family

Gene summary

Retinitis pigmentosa (RP) is a disease that leads to blindness by degeneration of cone photoreceptors. Rods produce factors required for cone viability. The protein encoded by this gene is one of those factors and is similar to a truncated form of thioredoxin. This gene has been proposed to have therapeutic value against RP. [provided by RefSeq, Dec 2015]

Previous symbols:

TXNL6

MANE transcript

NM_138454.2

Inheritance

—

ClinVar variants

U:43B:10

Top phenotype

NXNL1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr19:17,455,425-17,460,926

External References & Databases

Ensembl (ENSG00000171773)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Leber congenital amaurosisLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0018998

Submitter: Laboratory for Molecular Medicine

This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NXNL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 43

NXNL1-related disorderTotal: 8

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138454.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar		6
missense			43 clinvar	3 clinvar		46
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	10	0	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138454.2	RefSeq	NP_612463.1	2	MANE Select
ENST00000301944.3	Ensembl	ENSP00000305631.2	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell redox homeostasis
photoreceptor cell maintenance

Cellular Component

nuclear outer membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301944
Coding exons: 2
Length: 5530
Individuals with no LoFs: 125621
Homozygous LoFs: 0
Heterozygous LoFs: 39
Defined: 125660
p: 0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.191	125	131	0.953	0.00000760	1341
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00063	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000046	0.000044	rare
South Asian	0.00036	0.00036	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

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 (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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