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.

not_specified (55 variants)
not_provided (1 variants)
High_myopia (1 variants)
Abnormal_brain_morphology (1 variants)

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. These statistics are base on transcript: NM_000032727.4. 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				1 clinvar		1
missense		1 clinvar	56 clinvar			57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	56	1	0

Highest pathogenic variant AF is 0.00004102142

Loading clinvar variants...

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