LNX2

protein-coding

ligand of numb-protein X 2, the group of Ring finger proteins|PDZ domain containing

Gene summary

Enables identical protein binding activity. Predicted to be involved in nervous system development. Predicted to act upstream of or within neural precursor cell proliferation and neuron differentiation. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

PDZRN1

MANE transcript

NM_153371.4

Inheritance

—

ClinVar variants

U:100B:6

Top phenotype

Attention deficit hyperactivity disorder

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr13:27,545,913-27,620,529

External References & Databases

Ensembl (ENSG00000139517)

Transcript & Mutation Effects

hg38 • Region Span ~74.6 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 LNX2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 3

Attention deficit hyperactivity disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153371.4. 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	2 clinvar	1 clinvar	4
missense			97 clinvar	3 clinvar		100
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	100	5	1	106

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153371.4	RefSeq	NP_699202.1	9	MANE Select
ENST00000316334.5	Ensembl	ENSP00000325929.3	9	MANE Select
ENST00000649248.1	Ensembl	ENSP00000497224.1	9	Standard
ENST00000649248.2	Ensembl	ENSP00000497224.1	9	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
lnx2a	Danio rerio	Structure: anterior pancreatic bud Quality: decreased process quality abnormal

Gene / Model

Organism

Observed Phenotype

lnx2a

Danio rerio

Structure: anterior pancreatic bud

Quality: decreased process quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000316334
Coding exons: 9
Length: 74492
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.706	342	381	0.898	0.0000200	4512
Missense (PolyPhen)		128	185.08	0.6916		2188
Synonymous	-0.0901	151	150	1.01	0.00000859	1377
Loss of Function	2.91	14	31.7	0.442	0.00000204	345

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.629
RVIS EVS: -0.11
RVIS percentile EVS: 45.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.922

Gene Damage Prediction

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