KATNAL1

protein-coding

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

Gene summary

Enables identical protein binding activity and microtubule severing ATPase activity. Involved in microtubule severing. Located in cytosol and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032116.5

Inheritance

—

ClinVar variants

U:60B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr13:30,202,630-30,307,551

External References & Databases

Ensembl (ENSG00000102781)

Transcript & Mutation Effects

hg38 • Region Span ~104.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KATNAL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 55

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032116.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			56 clinvar	2 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	60	2	0	62

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032116.5	RefSeq	NP_115492.1	10	MANE Select
ENST00000380615.8	Ensembl	ENSP00000369989.3	10	MANE Select
NM_001014380.3	RefSeq	NP_001014402.1	10	Standard
ENST00000380617.7	Ensembl	ENSP00000369991.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
cytoplasmic microtubule organization
microtubule severing

Molecular Function

protein binding
ATP binding
microtubule binding
microtubule-severing ATPase activity
isomerase activity

Cellular Component

spindle pole
nucleus
cytoplasm
centrosome
spindle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380615
Coding exons: 10
Length: 104855
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125743
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.60	190	263	0.722	0.0000132	3198
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.811

Gene Damage Prediction

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