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 (461 variants)
not_specified (298 variants)
KATNIP-related_disorder (49 variants)
Joubert_syndrome_26 (27 variants)
Ciliopathy (3 variants)
Joubert_syndrome (1 variants)
Joubert_syndrome_1 (1 variants)
See_cases (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. These statistics are base on transcript: NM_000015202.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	154 clinvar	16 clinvar	175
missense		2 clinvar	353 clinvar	46 clinvar	11 clinvar	412
nonsense	5 clinvar	6 clinvar	1 clinvar			12
start loss						0
frameshift	10 clinvar	8 clinvar	1 clinvar			19
splice donor/acceptor (+/-2bp)		8 clinvar				8
Total	15	24	360	200	27

Highest pathogenic variant AF is 0.00028563922

Loading clinvar variants...

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

Biological process
Cellular component: extracellular space;cytoplasm;cytoskeleton;cell projection
Molecular function