KIAA1549

KIAA1549

Basic information

Region (hg38): 7:138831380-138981389

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

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 (1238 variants)
• Inborn genetic diseases (124 variants)
• Retinitis pigmentosa 86 (24 variants)
• not specified (3 variants)
• KIAA1549-related condition (2 variants)
• Retinitis pigmentosa (1 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.

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			9	369	38	416
missense			679	19	31	729
nonsense		1	2			3
start loss			1			1
frameshift	1	1	9			11
inframe indel			9			9
splice donor/acceptor (+/-2bp)			1			1
splice region			14	12	1	27
non coding			1	57	8	66
Total	1	2	711	445	77

Variants in KIAA1549

This is a list of pathogenic ClinVar variants found in the KIAA1549 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-138837915-G-A			Likely benign (Aug 16, 2022)
7-138837918-G-C			Uncertain significance (Apr 21, 2022)
7-138837926-C-T		Retinal dystrophy • Inborn genetic diseases	Uncertain significance (Oct 01, 2023)
7-138837927-G-A			Likely benign (Dec 17, 2023)
7-138837928-G-A			Uncertain significance (Jun 20, 2021)
7-138837933-C-G		Inborn genetic diseases	Uncertain significance (Oct 06, 2023)
7-138837937-T-C			Uncertain significance (Nov 08, 2022)
7-138837940-T-C			Uncertain significance (Oct 13, 2022)
7-138837944-A-C			Uncertain significance (Oct 03, 2023)
7-138837945-G-A			Likely benign (Jun 26, 2021)
7-138837949-C-T			Uncertain significance (Aug 09, 2022)
7-138837950-G-A		Inborn genetic diseases	Uncertain significance (Nov 27, 2023)
7-138837963-G-A			Likely benign (Jan 18, 2024)
7-138837963-G-T			Likely benign (Nov 13, 2023)
7-138837964-C-T			Uncertain significance (Feb 23, 2022)
7-138837965-G-A			Uncertain significance (Oct 08, 2021)
7-138837978-G-T			Likely benign (Jan 18, 2023)
7-138837980-G-C		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
7-138837981-A-G			Likely benign (Jul 13, 2022)
7-138837984-G-A			Likely benign (Jul 18, 2022)
7-138837987-C-T			Uncertain significance (Apr 08, 2021)
7-138837988-G-A		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
7-138837991-G-A			Uncertain significance (Feb 17, 2022)
7-138837994-T-C			Uncertain significance (May 22, 2023)
7-138837995-G-T			Uncertain significance (Nov 25, 2022)

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