KATNAL1

katanin catalytic subunit A1 like 1, the group of AAA ATPases

Basic information

Region (hg38): 13:30202629-30307551

Links

ENSG00000102781 ∙ NCBI:84056 ∙ OMIM:614764 ∙ HGNC:28361 ∙ Uniprot:Q9BW62 ∙ 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 KATNAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KATNAL1 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in KATNAL1

This is a list of pathogenic ClinVar variants found in the KATNAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-30208638-C-T		not specified	Uncertain significance (Mar 07, 2023)
13-30208640-T-A		not specified	Uncertain significance (Sep 23, 2023)
13-30210370-T-A		not specified	Uncertain significance (Sep 25, 2023)
13-30210431-C-T		not specified	Likely benign (Aug 16, 2022)
13-30210436-C-G		not specified	Uncertain significance (May 30, 2023)
13-30227425-T-C		not specified	Uncertain significance (Sep 14, 2022)
13-30227490-C-T		not specified	Uncertain significance (Jul 06, 2021)
13-30230503-C-A		not specified	Uncertain significance (Feb 27, 2024)
13-30230594-C-T		not specified	Uncertain significance (Feb 07, 2023)
13-30231330-C-T		not specified	Uncertain significance (Jun 22, 2024)
13-30231381-G-A		not specified	Uncertain significance (Sep 25, 2023)
13-30231382-A-G		not specified	Uncertain significance (Apr 24, 2024)
13-30240461-T-C		not specified	Uncertain significance (Feb 17, 2024)
13-30240504-T-C		not specified	Uncertain significance (Jul 05, 2023)
13-30241072-C-A		not specified	Uncertain significance (Oct 05, 2023)
13-30255472-T-C		not specified	Likely benign (Oct 10, 2023)
13-30255589-T-C		not specified	Uncertain significance (Jan 07, 2022)
13-30255603-C-G		not specified	Uncertain significance (Dec 16, 2022)
13-30280081-G-T		not specified	Uncertain significance (Aug 01, 2022)
13-30280183-C-A		not specified	Uncertain significance (Jan 31, 2023)
13-30283646-T-A		not specified	Uncertain significance (Mar 28, 2023)
13-30283702-T-C		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KATNAL1	protein_coding	protein_coding	ENST00000380615	10	104855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.532	0.468	125727	0	16	125743	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	190	263	0.722	0.0000132	3198
Missense in Polyphen		67	118.26	0.56655		1439
Synonymous	0.547	80	86.5	0.925	0.00000433	921
Loss of Function	3.59	5	23.9	0.209	0.00000132	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000879	0.0000879
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates microtubule dynamics in Sertoli cells, a process that is essential for spermiogenesis and male fertility. Severs microtubules in an ATP-dependent manner, promoting rapid reorganization of cellular microtubule arrays (By similarity). Has microtubule-severing activity in vitro (PubMed:26929214). {ECO:0000250|UniProtKB:Q8K0T4, ECO:0000269|PubMed:26929214}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.122
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.332
• hipred: Y
• hipred_score: 0.654
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Katnal1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

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