KATNAL2

katanin catalytic subunit A1 like 2, the group of AAA ATPases

Basic information

Region (hg38): 18:46917492-47103478

Links

ENSG00000167216 ∙ NCBI:83473 ∙ OMIM:614697 ∙ HGNC:25387 ∙ Uniprot:Q8IYT4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Disputed Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KATNAL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KATNAL2 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	16	3	20
missense			51	10	2	63
nonsense			2		1	3
start loss						0
frameshift			2		1	3
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region			2	5	1	8
non coding			77	19	1	97
Total	0	0	133	45	9

Variants in KATNAL2

This is a list of pathogenic ClinVar variants found in the KATNAL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-46946228-A-T		KATNAL2-related disorder	Likely benign (Apr 16, 2019)
18-46946253-T-A		KATNAL2-related disorder	Uncertain significance (Mar 21, 2024)
18-46946864-C-T		KATNAL2-related disorder	Uncertain significance (Jun 09, 2023)
18-46963179-C-T			Likely benign (Jun 01, 2023)
18-46963752-C-T			Likely benign (Feb 01, 2023)
18-47028556-T-C		ELOA3P-related condition	Likely benign (Oct 21, 2020)
18-47028616-G-A		ELOA3P-related condition	Likely benign (Dec 08, 2021)
18-47028776-T-G		ELOA3P-related condition	Likely benign (Feb 08, 2023)
18-47033023-T-C		not specified	Uncertain significance (Jan 16, 2024)
18-47033062-C-G		not specified	Uncertain significance (Jul 25, 2023)
18-47033073-G-A		not specified	Uncertain significance (Nov 17, 2023)
18-47033082-C-A		not specified	Uncertain significance (Oct 05, 2023)
18-47033091-G-T		not specified	Uncertain significance (May 20, 2024)
18-47033120-G-C		not specified	Uncertain significance (Nov 21, 2023)
18-47033234-C-A		not specified	Uncertain significance (Dec 04, 2023)
18-47033238-G-A		not specified	Uncertain significance (Jan 03, 2024)
18-47033319-T-C		not specified	Uncertain significance (Jun 28, 2022)
18-47033337-C-T		not specified	Likely benign (May 08, 2023)
18-47033343-A-G		not specified	Uncertain significance (Dec 27, 2023)
18-47033376-C-T		not specified	Uncertain significance (Mar 11, 2022)
18-47033406-C-G		not specified	Uncertain significance (Jan 09, 2024)
18-47033430-G-C		not specified	Likely benign (Mar 29, 2022)
18-47033515-A-C		not specified	Uncertain significance (Dec 14, 2021)
18-47033533-C-G		not specified	Uncertain significance (Dec 27, 2022)
18-47033559-C-A		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KATNAL2	protein_coding	protein_coding	ENST00000245121	14	130204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000118	0.988	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.421	244	263	0.927	0.0000147	3030
Missense in Polyphen		75	101.52	0.73879		1188
Synonymous	-1.31	115	98.5	1.17	0.00000559	880
Loss of Function	2.29	14	26.8	0.522	0.00000142	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000795	0.000795
Ashkenazi Jewish	0.00	0.00
East Asian	0.00261	0.00261
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.00261	0.00261
South Asian	0.000302	0.000294
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Severs microtubules in vitro in an ATP-dependent manner. This activity may promote rapid reorganization of cellular microtubule arrays. {ECO:0000255|HAMAP-Rule:MF_03025}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.208
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.11

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.266
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.209

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Katnal2

Gene ontology

• Biological process: cytoplasmic microtubule organization;microtubule severing
• Cellular component: spindle pole;nucleus;cytoplasm;spindle;microtubule
• Molecular function: protein binding;ATP binding;microtubule binding;microtubule-severing ATPase activity;isomerase activity;ATPase activity