LXN

protein-coding

latexin

Gene summary

This gene encodes the only known protein inhibitor of zinc-dependent metallocarboxypeptidases. The encoded protein, latexin, downregulates the population size of hematopoietic stem cells. This protein is found to be downregulated in cancer cells because of promoter hypermethylation. [provided by RefSeq, Jul 2020]

MANE transcript

NM_020169.4

Inheritance

—

ClinVar variants

U:23B:7

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr3:158,645,822-158,672,648

External References & Databases

Ensembl (ENSG00000079257)

Transcript & Mutation Effects

hg38 • Region Span ~26.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LXN variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 6

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020169.4. 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					1 clinvar	1
missense			19 clinvar	4 clinvar	2 clinvar	25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	23	4	3	30

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020169.4	RefSeq	NP_064554.3	6	MANE Select
ENST00000264265.4	Ensembl	ENSP00000264265.3	6	MANE Select
ENST00000482640.5	Ensembl	ENSP00000419373.1	4	Standard
ENST00001093529.1	Ensembl	ENSP00000763335.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

inflammatory response
negative regulation of endopeptidase activity
detection of temperature stimulus involved in sensory perception of pain

Molecular Function

protein binding
metalloendopeptidase inhibitor activity
heparin binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264265
Coding exons: 6
Length: 26872
Individuals with no LoFs: 125628
Homozygous LoFs: 1
Heterozygous LoFs: 119
Defined: 125748
p: 0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.748	89	111	0.800	0.00000498	1467
Missense (PolyPhen)		22	32.819	0.67034		422
Synonymous	0.187	40	41.5	0.963	0.00000221	393
Loss of Function	0.641	10	12.4	0.804	5.29e-7	150

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.0029	0.0028	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Hardly reversible, non-competitive, and potent inhibitor of CPA1, CPA2 and CPA4. May play a role in inflammation. {ECO:0000269|PubMed:15738388}.;

Recessive Scores

pRec: 0.173

Intolerance Scores

LoFtool: 0.813
RVIS EVS: 1.26
RVIS percentile EVS: 93.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.810

Gene Damage Prediction

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