KIAA1549

Basic information

Region (hg38): 7:138831381-138981389

Links

ENSG00000122778

∙ NCBI:57670 ∙ OMIM:613344 ∙ HGNC:22219 ∙ Uniprot:Q9HCM3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa 86 (Moderate), mode of inheritance: AR
retinitis pigmentosa (Supportive), mode of inheritance: AD
retinitis pigmentosa 86 (Strong), mode of inheritance: AR
retinitis pigmentosa (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 86	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	30120214

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIAA1549 gene.

not_provided (1330 variants)
Inborn_genetic_diseases (315 variants)
Retinal_dystrophy (99 variants)
KIAA1549-related_disorder (40 variants)
Retinitis_pigmentosa_86 (21 variants)
not_specified (3 variants)
Optic_atrophy (3 variants)
Retinitis_pigmentosa (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIAA1549 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001164665.2. 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	1 clinvar		11 clinvar	453 clinvar	28 clinvar	493
missense	1 clinvar	1 clinvar	792 clinvar	64 clinvar	17 clinvar	875
nonsense		2 clinvar	4 clinvar			6
start loss			1			1
frameshift	3 clinvar	2 clinvar	9 clinvar			14
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	5	6	818	517	45

Highest pathogenic variant AF is 0.0000061782043

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIAA1549	protein_coding	protein_coding	ENST00000422774	20	149939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0139	124645	0	29	124674	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0923	1121	1.11e+3	1.01	0.0000698	12426
Missense in Polyphen		388	445.27	0.87137		4725
Synonymous	-1.23	525	490	1.07	0.0000360	4249
Loss of Function	6.15	12	65.9	0.182	0.00000351	779

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000223	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000144	0.000142
Middle Eastern	0.000223	0.000223
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Disease: DISEASE: Note=A chromosomal aberration involving KIAA1549 is found in pilocytic astrocytoma. A tandem duplication of 2 Mb at 7q34 leads to the expression of a KIAA1549-BRAF fusion protein with a constitutive kinase activity and inducing cell transformation. {ECO:0000269|PubMed:18974108}.;
Pathway: Disease;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

pRec: 0.104

Intolerance Scores

loftool: 0.494
rvis_EVS: 1.66
rvis_percentile_EVS: 96.24

Haploinsufficiency Scores

pHI: 0.460
hipred: N
hipred_score: 0.270
ghis: 0.383

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0789

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: D630045J12Rik
Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); immune system phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: regulation of transcription by RNA polymerase II
Cellular component: plasma membrane;integral component of membrane
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific