KIAA0753

KIAA0753

Basic information

Region (hg38): 17:6578146-6640711

Links

ENSG00000198920 ∙ NCBI:9851 ∙ OMIM:617112 ∙ HGNC:29110 ∙ Uniprot:Q2KHM9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Jeune syndrome (Limited), mode of inheritance: AR
• orofaciodigital syndrome XV (Strong), mode of inheritance: AR
• orofaciodigital syndrome type 6 (Supportive), mode of inheritance: AR
• orofaciodigital syndrome XV (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Joubert syndrome 38; Short-rib thoracic dysplasia 21 without polydactyly	AR	Endocrine	An affected individual with Joubert syndrome has been described with manifestations including hypopituitarism, and some manifestations (eg, hypothyroidism) may benefit from medical management; Individuals with Short-rib thoracic dysplasia 21 without polydactyly have been described as having respiratory sequelae, including frequent infections, and awareness may allow aggressive pulmonary management	Craniofacial; Endocrine; Musculoskeletal; Neurologic	26643951; 28220259; 29138412; 31816441; 33875766; 34016807

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIAA0753 gene.

• not provided (336 variants)
• Inborn genetic diseases (46 variants)
• Orofaciodigital syndrome XV (14 variants)
• Joubert syndrome 38 (13 variants)
• Short-rib thoracic dysplasia 21 without polydactyly (13 variants)
• Joubert syndrome 38;Short-rib thoracic dysplasia 21 without polydactyly;Orofaciodigital syndrome XV (3 variants)
• not specified (2 variants)
• Jeune thoracic dystrophy (2 variants)
• Familial aplasia of the vermis;Jeune thoracic dystrophy (2 variants)
• Jeune thoracic dystrophy;Familial aplasia of the vermis (1 variants)
• KIAA0753-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIAA0753 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	51	10	62
missense		1	158	10	13	182
nonsense	6	5		1		12
start loss						0
frameshift	4	1				5
inframe indel						0
splice donor/acceptor (+/-2bp)		6				6
splice region			5	15	2	22
non coding				35	36	71
Total	10	13	159	97	59

Highest pathogenic variant AF is 0.000112

Variants in KIAA0753

This is a list of pathogenic ClinVar variants found in the KIAA0753 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-6579726-T-C		Joubert syndrome 38 • Orofaciodigital syndrome XV • Short-rib thoracic dysplasia 21 without polydactyly	Benign (Aug 19, 2021)
17-6579783-A-G			Likely benign (Oct 21, 2022)
17-6579788-C-G		Inborn genetic diseases	Uncertain significance (Jul 20, 2022)
17-6579812-G-C		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
17-6579813-A-T			Likely benign (Sep 27, 2022)
17-6579833-C-T			Uncertain significance (Mar 12, 2022)
17-6579862-A-T			Uncertain significance (Aug 16, 2022)
17-6589554-AAAG-A			Benign (May 13, 2021)
17-6589736-T-C			Benign (May 12, 2021)
17-6589759-G-A			Benign (Jan 28, 2024)
17-6589762-C-T			Likely benign (Sep 27, 2023)
17-6589763-G-GT			Likely benign (Sep 30, 2021)
17-6589772-T-C			Likely benign (Aug 14, 2023)
17-6589776-G-A			Uncertain significance (Sep 27, 2022)
17-6589784-A-T			Likely benign (Mar 01, 2023)
17-6589787-T-C			Benign (Jan 31, 2024)
17-6589792-G-A			Likely benign (Jan 15, 2024)
17-6589796-C-T			Likely benign (May 31, 2022)
17-6589797-G-A			Uncertain significance (Nov 03, 2016)
17-6589798-G-A			Uncertain significance (Oct 14, 2019)
17-6589800-T-C		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
17-6589809-C-G			Uncertain significance (Nov 27, 2023)
17-6589813-C-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2022)
17-6589814-A-G			Likely benign (Sep 12, 2023)
17-6589821-T-G		Inborn genetic diseases	Uncertain significance (Dec 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIAA0753	protein_coding	protein_coding	ENST00000361413	18	62780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-28	0.00196	124521	1	278	124800	0.00112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.207	517	530	0.975	0.0000284	6338
Missense in Polyphen		141	152.66	0.92361		1884
Synonymous	0.673	181	193	0.938	0.0000107	1847
Loss of Function	0.913	47	54.3	0.866	0.00000318	601

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0101	0.0100
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000556	0.000556
Finnish	0.000143	0.000139
European (Non-Finnish)	0.000604	0.000600
Middle Eastern	0.000556	0.000556
South Asian	0.000624	0.000621
Other	0.00134	0.00132

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in centriole duplication. Positively regulates CEP63 centrosomal localization. Required for WDR62 centrosomal localization and promotes the centrosomal localization of CDK2 (PubMed:24613305, PubMed:26297806). {ECO:0000269|PubMed:26297806}.
• Disease: DISEASE: Orofaciodigital syndrome 15 (OFD15) [MIM:617127]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD15 features include facial dysmorphism, lobulated tongue, clefting of the alveolar ridges, left hand postaxial polydactyly, broad right hallux and left hallux duplication, and intermittent respiratory difficulty. Brain anomalies include vermis hypoplasia with molar tooth sign, agenesis of corpus callosum, and ventricular dilation. OFD15 inheritance is autosomal recessive. {ECO:0000269|PubMed:26643951}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.583
• rvis_EVS: 2.14
• rvis_percentile_EVS: 97.96

Haploinsufficiency Scores

• pHI: 0.226
• hipred: N
• hipred_score: 0.144
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0491

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: 4933427D14Rik
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: si:dkey-243i1.1
• Affected structure: cranial cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: centriole replication;protein localization to centrosome
• Cellular component: centrosome;centriole;cytosol;centriolar satellite
• Molecular function: protein binding