NINL

ninein like, the group of EF-hand domain containing

Basic information

Region (hg38): 20:25451594-25585531

Links

ENSG00000101004 ∙ NCBI:22981 ∙ OMIM:609580 ∙ HGNC:29163 ∙ Uniprot:Q9Y2I6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NINL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NINL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			75	15	3	93
nonsense			2			2
start loss						0
frameshift				1		1
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	77	17	5

Variants in NINL

This is a list of pathogenic ClinVar variants found in the NINL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-25453456-CAG-C		NINL-related disorder	Likely benign (May 05, 2020)
20-25453465-C-T		not specified	Uncertain significance (Nov 23, 2021)
20-25453474-C-A		not specified	Uncertain significance (Dec 06, 2022)
20-25453498-G-C		not specified	Uncertain significance (Oct 19, 2024)
20-25453510-T-C		not specified	Uncertain significance (Feb 11, 2022)
20-25453599-T-C		not specified	Uncertain significance (Sep 26, 2023)
20-25453618-G-T		not specified	Uncertain significance (Dec 06, 2022)
20-25455675-G-T		not specified	Uncertain significance (Mar 14, 2023)
20-25458435-C-T		not specified	Uncertain significance (Nov 27, 2024)
20-25458439-G-A		not specified	Uncertain significance (Nov 17, 2023)
20-25458471-C-T		not specified	Likely benign (Apr 27, 2023)
20-25458472-G-A		not specified	Uncertain significance (Feb 23, 2023)
20-25458481-G-C		not specified	Uncertain significance (Nov 08, 2022)
20-25458482-C-A		not specified	Uncertain significance (Aug 26, 2024)
20-25458489-T-C		NINL-related disorder	Likely benign (Jul 28, 2022)
20-25461554-G-C		NINL-related disorder	Likely benign (Jul 27, 2020)
20-25461562-C-A		not specified	Uncertain significance (Jan 16, 2024)
20-25462412-C-T		not specified	Uncertain significance (Aug 10, 2021)
20-25462435-A-G		not specified	Uncertain significance (Mar 15, 2024)
20-25462445-G-A		not specified	Uncertain significance (Aug 17, 2021)
20-25462536-C-G		NINL-related disorder	Uncertain significance (Nov 02, 2022)
20-25467385-T-A		NINL-related disorder	Uncertain significance (Jan 30, 2024)
20-25467430-T-G		not specified	Uncertain significance (Dec 04, 2024)
20-25470033-C-T		not specified	Likely benign (Oct 17, 2023)
20-25470042-C-T		not specified	Uncertain significance (Sep 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NINL	protein_coding	protein_coding	ENST00000278886	23	132813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.65e-39	0.0000614	125547	1	200	125748	0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.976	900	821	1.10	0.0000535	8916
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00290	0.00290
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00321	0.00310
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000503	0.000484
Middle Eastern	0.00321	0.00310
South Asian	0.000859	0.000850
Other	0.000663	0.000652

dbNSFP

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}.
• Pathway: 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;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;PLK1 signaling events;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Intolerance Scores

• loftool: 0.979
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.277
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.455

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ninl
• Phenotype: growth/size/body region phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: ninl
• Affected structure: eye photoreceptor cell
• Phenotype tag: abnormal
• Phenotype quality: vacuolated

Gene ontology

• 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
• Cellular component: centrosome;cytosol;microtubule;intercellular bridge
• Molecular function: calcium ion binding;protein binding