INA

internexin neuronal intermediate filament protein alpha, the group of Intermediate filaments Type IV

Basic information

Region (hg38): 10:103277138-103290346

Previous symbols: [ "NEF5" ]

Links

ENSG00000148798 ∙ NCBI:9118 ∙ OMIM:605338 ∙ HGNC:6057 ∙ Uniprot:Q16352 ∙ 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 INA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INA 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
missense		1	25			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	25	1	0

Variants in INA

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

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

Position	Type	Phenotype	Significance	ClinVar
10-103277216-G-A		not specified	Uncertain significance (Jun 17, 2024)
10-103277219-T-G		not specified	Uncertain significance (Oct 25, 2024)
10-103277269-G-C		not specified	Uncertain significance (Nov 18, 2022)
10-103277321-G-A		not specified	Uncertain significance (Mar 12, 2024)
10-103277351-A-G		not specified	Uncertain significance (Nov 21, 2023)
10-103277357-C-T		not specified	Uncertain significance (Nov 03, 2022)
10-103277368-G-T		not specified	Uncertain significance (Jun 18, 2024)
10-103277404-G-A		not specified	Uncertain significance (Nov 13, 2023)
10-103277420-C-T		not specified	Uncertain significance (Aug 20, 2024)
10-103277461-A-G		not specified	Uncertain significance (Dec 20, 2023)
10-103277465-A-G		not specified	Uncertain significance (Dec 27, 2023)
10-103277526-C-A		not specified	Uncertain significance (Jan 23, 2023)
10-103277603-A-G		not specified	Uncertain significance (Dec 14, 2022)
10-103277683-A-G		not specified	Uncertain significance (Mar 28, 2023)
10-103277693-G-A		not specified	Uncertain significance (Feb 07, 2023)
10-103277720-G-A		not specified	Uncertain significance (Nov 24, 2024)
10-103277733-G-C		not specified	Uncertain significance (Oct 12, 2022)
10-103277770-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-103277773-G-A		Abnormal brain morphology	Likely pathogenic (-)
10-103277788-G-C		not specified	Uncertain significance (Jan 03, 2024)
10-103277818-G-A		not specified	Uncertain significance (Dec 04, 2024)
10-103277834-T-C		not specified	Uncertain significance (Mar 07, 2023)
10-103277919-C-A			Likely benign (Mar 02, 2018)
10-103277977-G-T		not specified	Uncertain significance (Aug 01, 2022)
10-103278010-G-A		High myopia	Uncertain significance (Dec 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INA	protein_coding	protein_coding	ENST00000369849	3	13189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-8	0.219	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	166	263	0.631	0.0000125	3132
Missense in Polyphen		61	106.03	0.57533		1248
Synonymous	1.41	100	120	0.836	0.00000587	1070
Loss of Function	0.419	13	14.7	0.882	6.29e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Class-IV neuronal intermediate filament that is able to self-assemble. It is involved in the morphogenesis of neurons. It may form an independent structural network without the involvement of other neurofilaments or it may cooperate with NF-L to form the filamentous backbone to which NF-M and NF-H attach to form the cross-bridges.

Recessive Scores

• pRec: 0.263

Intolerance Scores

• loftool: 0.191
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.694
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ina
• 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); normal phenotype

Zebrafish Information Network

• Gene name: inab
• Affected structure: VaP motor neuron
• Phenotype tag: abnormal
• Phenotype quality: branchiness

Gene ontology

• Biological process: substantia nigra development;cell differentiation;neurofilament cytoskeleton organization;postsynaptic actin cytoskeleton organization;postsynaptic intermediate filament cytoskeleton organization;cellular response to leukemia inhibitory factor
• Cellular component: extracellular space;nucleoplasm;neurofilament;nuclear membrane;cytoplasmic ribonucleoprotein granule;myelin sheath;intermediate filament cytoskeleton;Schaffer collateral - CA1 synapse;postsynapse
• Molecular function: structural constituent of cytoskeleton;structural constituent of postsynaptic actin cytoskeleton;structural constituent of postsynaptic intermediate filament cytoskeleton