NIN

ninein, the group of EF-hand domain containing

Basic information

Region (hg38): 14:50719762-50831162

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 (448 variants)
• Inborn genetic diseases (87 variants)
• not specified (64 variants)
• Seckel syndrome 7 (29 variants)
• Seckel syndrome (3 variants)
• NIN-related condition (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.

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	77	20	98
missense			250	18	17	285
nonsense		2	2			4
start loss						0
frameshift	1		7			8
inframe indel			5			5
splice donor/acceptor (+/-2bp)			1			1
splice region			2	11	5	18
non coding		1	2	28	61	92
Total	1	3	268	123	98

Highest pathogenic variant AF is 0.00000657

Variants in NIN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-50723492-A-G			Likely benign (Jan 25, 2024)
14-50723493-T-C			Likely benign (Apr 01, 2023)
14-50723501-G-T			Uncertain significance (Jan 01, 2024)
14-50723558-T-C			Uncertain significance (Jan 09, 2024)
14-50723570-C-T			Uncertain significance (Mar 20, 2022)
14-50723576-T-C		not specified	Uncertain significance (Oct 12, 2021)
14-50723590-G-A		Seckel syndrome 7	Uncertain significance (Jan 04, 2024)
14-50723607-C-T			Likely benign (Dec 25, 2022)
14-50723610-C-T			Likely benign (May 21, 2018)
14-50723621-T-C			Uncertain significance (Nov 01, 2012)
14-50723640-C-G			Likely benign (Dec 02, 2022)
14-50723642-C-A			Uncertain significance (Nov 01, 2022)
14-50723659-G-C		not specified	Uncertain significance (Aug 12, 2021)
14-50725777-G-A			Benign (May 13, 2021)
14-50725853-G-C			Benign (May 14, 2021)
14-50725940-C-T			Likely benign (Oct 05, 2022)
14-50725941-G-A		Seckel syndrome 7	Benign (Jan 31, 2024)
14-50725989-C-A			Uncertain significance (Jul 06, 2023)
14-50725989-C-G		not specified	Uncertain significance (Aug 02, 2021)
14-50725990-C-G		not specified	Uncertain significance (Nov 10, 2022)
14-50725991-T-C		NIN-related disorder • not specified	Conflicting classifications of pathogenicity (Jan 24, 2024)
14-50726007-T-A		not specified	Uncertain significance (Jun 29, 2023)
14-50726030-G-A		Seckel syndrome 7	Likely pathogenic (Jun 20, 2019)
14-50726038-A-AT			Uncertain significance (Nov 22, 2023)
14-50726048-C-A		not specified	Uncertain significance (Dec 09, 2023)

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