NINL

protein-coding

ninein like, the group of EF-hand domain containing

Gene summary

Predicted to enable calcium ion binding activity. Predicted to be involved in microtubule anchoring at centrosome. Located in centrosome and cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_025176.6

Inheritance

—

ClinVar variants

U:231B:36

Top phenotype

NINL-related disorder

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr20:25,451,594-25,585,531

External References & Databases

Ensembl (ENSG00000101004)

Transcript & Mutation Effects

hg38 • Region Span ~133.9 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 NINL variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 229

NINL-related disorderTotal: 18

not providedTotal: 5

Autism spectrum disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025176.6. 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			3 clinvar	2 clinvar		5
missense			216 clinvar	31 clinvar	2 clinvar	249
nonsense			4 clinvar			4
start loss						0
frameshift			1 clinvar	1 clinvar		2
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	231	34	2	267

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 71 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025176.6	RefSeq	NP_079452.3	23	MANE Select
ENST00000278886.11	Ensembl	ENSP00000278886.6	23	MANE Select
NM_001318226.2	RefSeq	NP_001305155.1	22	Standard
ENST00000336104.6	Ensembl	ENSP00000338621.6	15	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ninl	Danio rerio	Structure: eye photoreceptor cell Quality: vacuolated abnormal

Gene / Model

Organism

Observed Phenotype

ninl

Danio rerio

Structure: eye photoreceptor cell

Quality: vacuolated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Regulation of PLK1 Activity at G2/M Transition
Recruitment of mitotic centrosome proteins and complexes
Loss of Nlp from mitotic centrosomes
Loss of proteins required for interphase microtubule organization from the centrosome
Centrosome maturation

Biological Process

G2/M transition of mitotic cell cycle
regulation of G2/M transition of mitotic cell cycle
microtubule anchoring at centrosome
ciliary basal body-plasma membrane docking

Molecular Function

calcium ion binding
protein binding

Cellular Component

centrosome
cytosol
microtubule
intercellular bridge

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278886
Coding exons: 23
Length: 132813
Individuals with no LoFs: 125547
Homozygous LoFs: 1
Heterozygous LoFs: 200
Defined: 125748
p: 0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.976	900	821	1.10	0.0000535	8916
Missense (PolyPhen)		142	130.65	1.0869		1716
Synonymous	-1.58	404	366	1.10	0.0000255	2737
Loss of Function	0.892	64	72.2	0.887	0.00000346	791

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0023	notable
Latino/Admixed American	0.00056	0.00055	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0032	0.0031	notable
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00050	0.00048	rare
South Asian	0.00086	0.00085	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the microtubule organization in interphase cells. Overexpression induces the fragmentation of the Golgi, and causes lysosomes to disperse toward the cell periphery; it also interferes with mitotic spindle assembly. May play a role in ovarian carcinogenesis. {ECO:0000269|PubMed:12852856, ECO:0000269|PubMed:16254247, ECO:0000269|PubMed:18538832}.;

Intolerance Scores

LoFtool: 0.979
RVIS EVS: 1.42
RVIS percentile EVS: 94.94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.455

Gene Damage Prediction

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