KIAA0319L

protein-coding

KIAA0319 like

Gene summary

Predicted to be involved in neuron migration. Located in cytoplasmic vesicle; plasma membrane; and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024874.5

Inheritance

—

ClinVar variants

U:102B:22

Top phenotype

systemic lupus erythematosus

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr1:35,393,883-35,557,950

External References & Databases

Ensembl (ENSG00000142687)

Transcript & Mutation Effects

hg38 • Region Span ~164.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

systemic lupus erythematosusSUPPORTIVE

Inheritance Pattern: Unknown

Disease ID:MONDO:0007915

Submitter: Orphanet

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIAA0319L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024874.5. 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				5 clinvar	1 clinvar	6
missense			98 clinvar	15 clinvar	1 clinvar	114
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	102	20	2	124

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 144 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024874.5	RefSeq	NP_079150.3	20	MANE Select
ENST00000325722.8	Ensembl	ENSP00000318406.3	20	MANE Select
ENST00000426982.7	Ensembl	ENSP00000395883.3	20	Standard
ENST00000431916.5	Ensembl	ENSP00000393862.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

Golgi membrane
plasma membrane
integral component of membrane
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325722
Coding exons: 20
Length: 124461
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.56	455	559	0.814	0.0000277	6876
Missense (PolyPhen)		112	187.75	0.59653		2318
Synonymous	1.88	185	220	0.839	0.0000118	2062
Loss of Function	4.81	16	54.2	0.295	0.00000271	609

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible role in axon guidance through interaction with RTN4R. {ECO:0000269|PubMed:20697954}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.760
RVIS EVS: -0.84
RVIS percentile EVS: 11.4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.794

Gene Damage Prediction

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