NIN

ninein, the group of EF-hand domain containing

Basic information

Region (hg38): 14:50719763-50831162

Links

ENSG00000100503

∙ NCBI:51199 ∙ OMIM:608684 ∙ HGNC:14906 ∙ Uniprot:Q8N4C6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Seckel syndrome 7 (Limited), mode of inheritance: AR
Seckel syndrome 7 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Seckel syndrome 7	AR	Endocrine	The condition can include manifestations including endocrine anomalies (eg, hypothyroidism, hypogonadism), some of which may respond to appropriate hormonal therapy (eg, thyroid hormone replacemetn therapy, estrogen therapy)	Craniofacial; Endocrine; Musculoskeletal; Neurologic	22933543

ClinVar

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

not_provided (696 variants)
not_specified (305 variants)
NIN-related_disorder (31 variants)
Seckel_syndrome_7 (18 variants)
Seckel_syndrome (3 variants)
Joubert_syndrome_3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020921.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	156 clinvar	12 clinvar	171
missense			506 clinvar	40 clinvar	12 clinvar	558
nonsense		2 clinvar	7 clinvar			9
start loss						0
frameshift	1 clinvar		12 clinvar			13
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	1	2	531	196	24

Highest pathogenic variant AF is 0.0000191566

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIN	protein_coding	protein_coding	ENST00000382041	28	111359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.63e-9	1.00	125652	1	95	125748	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	1049	1.08e+3	0.972	0.0000589	13881
Missense in Polyphen		300	349.41	0.85858		4897
Synonymous	1.02	390	417	0.936	0.0000233	3730
Loss of Function	6.59	36	111	0.325	0.00000588	1317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000633	0.000628
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000328	0.000326
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000496	0.000492
Middle Eastern	0.000328	0.000326
South Asian	0.000461	0.000457
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Centrosomal protein required in the positioning and anchorage of the microtubule minus-end in epithelial cells (PubMed:15190203, PubMed:23386061). May also act as a centrosome maturation factor (PubMed:11956314). May play a role in microtubule nucleation, by recruiting the gamma-tubulin ring complex to the centrosome (PubMed:15190203). Overexpression does not perturb nucleation or elongation of microtubules but suppresses release of microtubules (PubMed:15190203). Required for centriole organization and microtubule anchoring at the mother centriole (PubMed:23386061). {ECO:0000269|PubMed:11956314, ECO:0000269|PubMed:15190203, ECO:0000269|PubMed:23386061}.;
Disease: DISEASE: Seckel syndrome 7 (SCKL7) [MIM:614851]: A rare autosomal recessive disorder characterized by proportionate dwarfism of prenatal onset associated with low birth weight, growth retardation, severe microcephaly with a bird-headed like appearance, and mental retardation. {ECO:0000269|PubMed:22933543}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.175

Intolerance Scores

loftool: 0.943
rvis_EVS: 0.07
rvis_percentile_EVS: 59.05

Haploinsufficiency Scores

pHI: 0.242
hipred: Y
hipred_score: 0.547
ghis: 0.614

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.534

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nin
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: nin
Affected structure: otolith
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: protein localization;centriole-centriole cohesion;corpus callosum morphogenesis;corticospinal tract morphogenesis;positive regulation of microtubule polymerization;microtubule anchoring at centrosome;collateral sprouting;positive regulation of axonogenesis;centrosome localization;centrosome-templated microtubule nucleation
Cellular component: pericentriolar material;spindle pole;nucleus;nucleolus;centrosome;centriole;plasma membrane;dendrite;microtubule minus-end;axonal growth cone;apical part of cell;mitotic spindle;mitotic spindle pole;ciliary transition fiber;centriolar subdistal appendage
Molecular function: calcium ion binding;protein binding;GTP binding;kinase binding