KATNIP

katanin interacting protein

Basic information

Region (hg38): 16:27550133-27780344

Previous symbols: [ "KIAA0556" ]

Links

ENSG00000047578 ∙ NCBI:23247 ∙ OMIM:616650 ∙ HGNC:29068 ∙ Uniprot:O60303 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Joubert syndrome (Supportive), mode of inheritance: AR
• Joubert syndrome 26 (Strong), mode of inheritance: AR
• ciliopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Joubert syndrome 26	AR	Endocrine	Individuals have been described with panhypopituitarism, and awareness may allow early diagnosis and medical management (eg, with hormone replacement therapy)	Endocrine; Neurologic	26714646

ClinVar

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

• not provided (7 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KATNIP 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			3	121	21	145
missense			238	33	17	288
nonsense	1	4	1			6
start loss						0
frameshift	7	3	2			12
inframe indel			1			1
splice donor/acceptor (+/-2bp)		6				6
splice region			7	14	3	24
non coding				34	23	57
Total	8	13	245	188	61

Highest pathogenic variant AF is 0.0000131

Variants in KATNIP

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

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

Position	Type	Phenotype	Significance	ClinVar
16-27550169-G-A			Conflicting classifications of pathogenicity (Jun 01, 2023)
16-27550189-TG-T			Benign (Jan 02, 2024)
16-27550194-C-T			Likely benign (Jan 06, 2024)
16-27550263-G-A			Benign (Nov 12, 2018)
16-27573883-G-A			Likely benign (Jun 14, 2022)
16-27573895-C-T			Likely benign (Jul 14, 2023)
16-27573896-G-T			Uncertain significance (Aug 20, 2022)
16-27573912-C-T		Joubert syndrome 26	Pathogenic (Apr 19, 2024)
16-27573915-A-G			Uncertain significance (Mar 18, 2022)
16-27573918-G-GC		See cases	Likely pathogenic (Apr 24, 2020)
16-27573919-C-A		not specified	Uncertain significance (Aug 30, 2023)
16-27573920-C-G			Benign (Jan 22, 2024)
16-27573921-G-A		not specified	Uncertain significance (May 03, 2023)
16-27573939-T-G		not specified	Uncertain significance (Aug 02, 2022)
16-27573942-C-T		Joubert syndrome 26	Pathogenic/Likely pathogenic (Mar 17, 2024)
16-27573965-G-T			Likely benign (Mar 29, 2018)
16-27573967-C-T			Likely benign (Jun 28, 2022)
16-27573973-C-A			Likely benign (Nov 22, 2023)
16-27573974-G-A			Likely benign (Mar 20, 2022)
16-27618340-G-C			Benign (Nov 12, 2018)
16-27618431-G-A		not specified	Likely benign (Jan 04, 2024)
16-27618467-G-T			Uncertain significance (Jun 27, 2022)
16-27618487-T-C			Likely benign (Dec 31, 2021)
16-27618501-G-A		not specified	Uncertain significance (Mar 17, 2022)
16-27618512-C-G			Likely benign (Oct 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KATNIP	protein_coding	protein_coding	ENST00000261588	28	230237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-29	0.267	125415	1	332	125748	0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.111	987	977	1.01	0.0000604	10569
Missense in Polyphen		329	356.56	0.92271		3987
Synonymous	-0.176	417	412	1.01	0.0000286	3194
Loss of Function	2.23	57	78.3	0.728	0.00000422	863

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00207	0.00206
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000599	0.000598
Finnish	0.000649	0.000647
European (Non-Finnish)	0.00152	0.00150
Middle Eastern	0.000599	0.000598
South Asian	0.00220	0.00219
Other	0.00279	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May influence the stability of microtubules (MT), possibly through interaction with the MT-severing katanin complex. {ECO:0000269|PubMed:26714646}.
• Disease: DISEASE: Joubert syndrome 26 (JBTS26) [MIM:616784]: A form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. JBTS26 inheritance is autosomal recessive. {ECO:0000269|PubMed:26714646}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• loftool: 0.918
• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.13

Haploinsufficiency Scores

• pHI: 0.247
• hipred: N
• hipred_score: 0.306
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.361

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: D430042O09Rik
• 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)

Gene ontology

• Cellular component: extracellular space;cytoplasm;cytoskeleton;cell projection