KIAA0319

KIAA0319

Basic information

Region (hg38): 6:24544104-24646191

Links

ENSG00000137261 ∙ NCBI:9856 ∙ OMIM:609269 ∙ HGNC:21580 ∙ Uniprot:Q5VV43 ∙ 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 KIAA0319 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIAA0319 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				4	4	8
missense			49	8	5	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			4	3		7
Total	0	0	53	15	9

Variants in KIAA0319

This is a list of pathogenic ClinVar variants found in the KIAA0319 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-24547161-G-A		KIAA0319-related disorder	Likely benign (May 21, 2020)
6-24547193-G-A		not specified	Uncertain significance (Jun 28, 2024)
6-24547202-T-C		not specified	Uncertain significance (May 24, 2023)
6-24547296-C-T		not specified	Uncertain significance (Sep 30, 2024)
6-24547299-A-T		not specified	Uncertain significance (Jul 14, 2023)
6-24547310-C-A		not specified	Uncertain significance (Aug 12, 2024)
6-24547331-C-T		not specified	Uncertain significance (Jun 02, 2024)
6-24547332-G-T			Likely benign (Mar 01, 2024)
6-24551436-T-C		KIAA0319-related disorder	Benign (Dec 23, 2019)
6-24551440-T-C		not specified	Uncertain significance (Jan 04, 2022)
6-24551501-T-C		KIAA0319-related disorder	Benign (Dec 23, 2019)
6-24554534-T-C		KIAA0319-related disorder	Benign (Oct 17, 2019)
6-24554616-T-C		not specified	Uncertain significance (Dec 10, 2024)
6-24556631-T-C		not specified	Uncertain significance (Mar 22, 2022)
6-24556678-C-T		not specified	Uncertain significance (May 15, 2024)
6-24556705-T-C		not specified	Uncertain significance (Sep 29, 2023)
6-24556708-C-G		KIAA0319-related disorder	Benign (Aug 14, 2017)
6-24559010-T-C		KIAA0319-related disorder	Likely benign (Dec 30, 2019)
6-24559031-A-C		not specified	Uncertain significance (Nov 10, 2024)
6-24559052-C-G		not specified	Uncertain significance (May 13, 2022)
6-24559053-A-G		KIAA0319-related disorder	Benign (Oct 30, 2019)
6-24559057-T-C		not specified	Uncertain significance (Aug 10, 2023)
6-24559074-C-G		not specified	Uncertain significance (May 20, 2024)
6-24559128-G-T		not specified	Uncertain significance (May 08, 2024)
6-24563368-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIAA0319	protein_coding	protein_coding	ENST00000378214	20	102052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.32e-20	0.206	125627	0	121	125748	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	567	599	0.947	0.0000320	6969
Missense in Polyphen		171	199.81	0.8558		2453
Synonymous	1.46	214	243	0.881	0.0000143	2152
Loss of Function	1.59	37	49.0	0.755	0.00000241	570

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00110
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000639	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000496	0.000484
Middle Eastern	0.000639	0.000598
South Asian	0.000723	0.000719
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in neuronal migration during development of the cerebral neocortex. May function in a cell autonomous and a non- cell autonomous manner and play a role in appropriate adhesion between migrating neurons and radial glial fibers. May also regulate growth and differentiation of dendrites. {ECO:0000269|PubMed:19679544}.
• Disease: DISEASE: Dyslexia 2 (DYX2) [MIM:600202]: A relatively common, complex cognitive disorder characterized by an impairment of reading performance despite adequate motivational, educational and intellectual opportunities. It is a multifactorial trait, with evidence for familial clustering and heritability. {ECO:0000269|PubMed:16600991}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.0879

Intolerance Scores

• loftool: 0.943
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.31

Haploinsufficiency Scores

• pHI: 0.292
• hipred: N
• hipred_score: 0.306
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: D130043K22Rik
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: neuron migration;membrane organization;negative regulation of dendrite development
• Cellular component: early endosome;plasma membrane;integral component of membrane;clathrin-coated vesicle membrane;cytoplasmic vesicle;early endosome membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding