KATNA1

katanin catalytic subunit A1, the group of AAA ATPases

Basic information

Region (hg38): 6:149594872-149648972

Links

ENSG00000186625 ∙ NCBI:11104 ∙ OMIM:606696 ∙ HGNC:6216 ∙ Uniprot:O75449 ∙ 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 KATNA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KATNA1 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						0
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in KATNA1

This is a list of pathogenic ClinVar variants found in the KATNA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149595054-A-C		not specified	Uncertain significance (Nov 23, 2022)
6-149595229-G-C		not specified	Uncertain significance (May 10, 2024)
6-149597123-A-G		not specified	Uncertain significance (Feb 12, 2024)
6-149597163-T-C		not specified	Uncertain significance (Oct 02, 2023)
6-149597526-G-C		not specified	Uncertain significance (Oct 27, 2022)
6-149598349-G-C		not specified	Uncertain significance (Nov 14, 2023)
6-149601610-C-T		not specified	Uncertain significance (Apr 07, 2022)
6-149601691-G-A		not specified	Uncertain significance (Oct 06, 2021)
6-149601737-C-T		not specified	Uncertain significance (Oct 03, 2023)
6-149603289-C-A		not specified	Uncertain significance (Feb 13, 2024)
6-149603342-T-G		not specified	Uncertain significance (Jun 06, 2023)
6-149603348-C-G		not specified	Uncertain significance (Nov 17, 2023)
6-149604734-T-C		not specified	Uncertain significance (May 31, 2023)
6-149604769-G-A		not specified	Uncertain significance (Jul 19, 2023)
6-149623147-G-A		not specified	Uncertain significance (Jun 11, 2024)
6-149623168-T-C		not specified	Uncertain significance (Nov 15, 2021)
6-149623216-G-A		not specified	Uncertain significance (Nov 28, 2023)
6-149623218-C-T		not specified	Uncertain significance (Jun 11, 2024)
6-149623221-T-C		not specified	Uncertain significance (Mar 23, 2022)
6-149632760-T-C		not specified	Uncertain significance (Feb 27, 2023)
6-149632793-C-T		not specified	Uncertain significance (Aug 30, 2022)
6-149632825-G-A		not specified	Uncertain significance (Oct 18, 2021)
6-149632826-C-G		not specified	Uncertain significance (Jan 31, 2023)
6-149638477-G-A		not specified	Uncertain significance (Apr 25, 2023)
6-149638483-T-C		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KATNA1	protein_coding	protein_coding	ENST00000367411	10	54100

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000168	0.999	125663	0	84	125747	0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	200	282	0.709	0.0000157	3213
Missense in Polyphen		73	122.92	0.59389		1334
Synonymous	0.402	90	95.0	0.947	0.00000531	922
Loss of Function	2.81	13	29.5	0.441	0.00000194	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000706	0.000704
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000110	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000504	0.000501
Middle Eastern	0.000110	0.000109
South Asian	0.000166	0.000163
Other	0.000338	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of a complex which severs microtubules in an ATP-dependent manner. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation. Microtubule release from the mitotic spindle poles may allow depolymerization of the microtubule end proximal to the spindle pole, leading to poleward microtubule flux and poleward motion of chromosome. Microtubule release within the cell body of neurons may be required for their transport into neuronal processes by microtubule-dependent motor proteins. This transport is required for axonal growth. {ECO:0000255|HAMAP-Rule:MF_03023, ECO:0000269|PubMed:10751153, ECO:0000269|PubMed:11870226, ECO:0000269|PubMed:19287380}.
• Pathway: Lissencephaly gene (LIS1) in neuronal migration and development (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.328
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.251
• hipred: Y
• hipred_score: 0.706
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.632

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Katna1

Zebrafish Information Network

• Gene name: katna1
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: cell cycle;cytoplasmic microtubule organization;microtubule severing;cell division
• Cellular component: spindle pole;nucleus;cytoplasm;centrosome;spindle;microtubule;midbody;mitotic spindle pole
• Molecular function: protein binding;ATP binding;microtubule binding;microtubule-severing ATPase activity;isomerase activity;ATPase activity;protein heterodimerization activity