KIAA1586

KIAA1586

Basic information

Region (hg38): 6:57046532-57059041

Links

ENSG00000168116 ∙ NCBI:57691 ∙ ∙ HGNC:21360 ∙ Uniprot:Q9HCI6 ∙ 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 KIAA1586 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIAA1586 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						0
missense			41	4		45
nonsense				2		2
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	7	0

Variants in KIAA1586

This is a list of pathogenic ClinVar variants found in the KIAA1586 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-57046766-C-T		not specified	Uncertain significance (Oct 01, 2024)
6-57046771-T-A		not specified	Uncertain significance (Dec 04, 2023)
6-57046775-A-T		not specified	Uncertain significance (Nov 15, 2024)
6-57050775-A-G		not specified	Uncertain significance (Sep 27, 2021)
6-57050777-G-A		not specified	Uncertain significance (Apr 05, 2023)
6-57050784-C-T		not specified	Likely benign (Jan 18, 2022)
6-57050804-A-G		not specified	Uncertain significance (Jun 10, 2022)
6-57050808-A-G		not specified	Uncertain significance (Aug 18, 2021)
6-57050834-C-T		not specified	Uncertain significance (May 09, 2023)
6-57050840-G-A		not specified	Likely benign (Feb 28, 2023)
6-57052686-A-T		not specified	Uncertain significance (Mar 31, 2024)
6-57052710-C-T		KIAA1586-related disorder	Likely benign (Jul 15, 2021)
6-57052711-G-A		not specified	Uncertain significance (Oct 03, 2022)
6-57052716-G-C		not specified	Uncertain significance (May 04, 2022)
6-57052755-A-C		not specified	Uncertain significance (Oct 06, 2021)
6-57052772-T-A		not specified	Uncertain significance (Jun 01, 2023)
6-57052830-A-G		not specified	Likely benign (Sep 07, 2022)
6-57052923-G-A		not specified	Uncertain significance (Jan 16, 2024)
6-57052950-T-C		not specified	Uncertain significance (Dec 04, 2024)
6-57053014-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-57053053-T-C		not specified	Uncertain significance (May 01, 2024)
6-57053109-C-T		KIAA1586-related disorder	Likely benign (Mar 15, 2021)
6-57053114-A-T		not specified	Uncertain significance (Feb 13, 2024)
6-57053116-A-G		not specified	Uncertain significance (Sep 13, 2023)
6-57053128-A-G		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIAA1586	protein_coding	protein_coding	ENST00000370733	4	8677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.75e-11	0.385	124688	8	1051	125747	0.00422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.544	404	374	1.08	0.0000179	5193
Missense in Polyphen		82	88.475	0.92682		1327
Synonymous	0.513	125	133	0.943	0.00000647	1436
Loss of Function	1.09	19	24.8	0.765	0.00000126	407

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0401	0.0356
Ashkenazi Jewish	0.000425	0.000397
East Asian	0.00326	0.00321
Finnish	0.000186	0.000185
European (Non-Finnish)	0.00183	0.00174
Middle Eastern	0.00326	0.00321
South Asian	0.00598	0.00550
Other	0.00249	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 SUMO-protein ligase; facilitates UBE2I/UBC9-mediated SUMO2 modification of target proteins (PubMed:26524493).

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.3

Haploinsufficiency Scores

• pHI: 0.0825
• hipred: N
• hipred_score: 0.123
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Gene ontology

• Biological process: protein sumoylation
• Molecular function: SUMO ligase activity