LTN1

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			1 clinvar	4 clinvar		5
missense			200 clinvar	11 clinvar	2 clinvar	213
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	208	15	2	225

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015565.3	RefSeq	NP_056380.3	30	MANE Select
ENST00000361371.10	Ensembl	ENSP00000354977.4	30	MANE Select
NM_001320766.2	RefSeq	NP_001307695.2	29	Standard
ENST00000389194.7	Ensembl	ENSP00000373846.3	30	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
Immune System
Adaptive Immune System

Biological Process

proteasome-mediated ubiquitin-dependent protein catabolic process
protein autoubiquitination
rescue of stalled ribosome
ribosome-associated ubiquitin-dependent protein catabolic process

Molecular Function

protein binding
zinc ion binding
ribosomal large subunit binding
ubiquitin protein ligase activity

Cellular Component

cytosol
RQC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389194
Coding exons: 30
Length: 64805
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125748
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	738	898	0.822	0.0000444	11841
Missense (PolyPhen)		170	277.49	0.61264		3717
Synonymous	0.404	319	328	0.972	0.0000165	3406
Loss of Function	6.38	22	85.8	0.256	0.00000431	1165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00024	0.00023	rare
South Asian	0.00015	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23685075, PubMed:25132172, PubMed:25578875). Ubiquitination leads to VCP/p97 recruitment for extraction and degradation of the incomplete translation product (By similarity). {ECO:0000250|UniProtKB:Q04781, ECO:0000269|PubMed:23685075, ECO:0000269|PubMed:25132172, ECO:0000269|PubMed:25578875}.;

Recessive Scores

pRec: 0.0993

Intolerance Scores

RVIS EVS: 0.26
RVIS percentile EVS: 70.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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