LNPK

protein-coding

lunapark, ER junction formation factor

Gene summary

Enables identical protein binding activity. Involved in endoplasmic reticulum tubular network maintenance and positive regulation of endoplasmic reticulum tubular network organization. Located in endoplasmic reticulum tubular network membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA1715

MANE transcript

NM_030650.3

Inheritance

ClinVar variants

P:17U:19B:14

Top phenotype

Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr2:175,923,882-176,002,839

External References & Databases

Ensembl (ENSG00000144320)

Transcript & Mutation Effects

hg38 • Region Span ~79.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060761

Submitter: Ambry Genetics

neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060761

Submitter: Labcorp Genetics (formerly Invitae)

neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060761

Submitter: PanelApp Australia

neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0060761

Submitter: G2P

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumAR

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 30032983

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LNPK variants in ClinVar

5 Conditions Cataloged

Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumTotal: 27

not providedTotal: 19

not specifiedTotal: 14

LNPK-related disorderTotal: 9

Inborn genetic diseasesTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030650.3. 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				7 clinvar		7
missense			12 clinvar	7 clinvar		19
nonsense	3 clinvar	2 clinvar	1 clinvar			6
start loss						0
frameshift	4 clinvar	4 clinvar	1 clinvar			9
splice donor/acceptor (+/-2bp)	4 clinvar		5 clinvar			9
Total	11	6	19	14	0	50

Highest pathogenic variant AF is 0.000036257316

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_030650.3	RefSeq	NP_085153.1	12	MANE Select
ENST00000272748.9	Ensembl	ENSP00000272748.4	12	MANE Select
NM_001305008.1	RefSeq	NP_001291937.1	13	Standard
NM_001305009.1	RefSeq	NP_001291938.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

blood coagulation
regulation of chondrocyte differentiation
embryonic forelimb morphogenesis
embryonic digit morphogenesis
limb development

Molecular Function

identical protein binding
metal ion binding

Cellular Component

nucleoplasm
endoplasmic reticulum
endoplasmic reticulum membrane
integral component of membrane
integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272748
Coding exons: 12
Length: 78948
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.549	189	211	0.894	0.00000993	2740
Missense (PolyPhen)		43	50.854	0.84556		664
Synonymous	-0.515	79	73.4	1.08	0.00000359	840
Loss of Function	2.90	10	25.9	0.386	0.00000148	319

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00014	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Endoplasmic reticulum (ER)-shaping membrane protein that plays a role in determining ER morphology. Involved in the stabilization of nascent three-way ER tubular junctions within the ER network (PubMed:24223779, PubMed:25404289, PubMed:25548161, PubMed:27619977). May also play a role as a curvature-stabilizing protein within the three-way ER tubular junction network (PubMed:25404289). May be involved in limb and central nervous system development (By similarity). {ECO:0000250|UniProtKB:Q7TQ95, ECO:0000269|PubMed:24223779, ECO:0000269|PubMed:25404289, ECO:0000269|PubMed:25548161, ECO:0000269|PubMed:27619977}.;

Recessive Scores

pRec: 0.280

Intolerance Scores

RVIS EVS: 0.22
RVIS percentile EVS: 68.13

Essentials

Essential (gene trap): N