KIAA1522

KIAA1522

Basic information

Region (hg38): 1:32741829-32774970

Links

ENSG00000162522 ∙ NCBI:57648 ∙ ∙ HGNC:29301 ∙ Uniprot:Q9P206 ∙ 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 KIAA1522 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIAA1522 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				1		1
missense			78	5		83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	78	6	0

Variants in KIAA1522

This is a list of pathogenic ClinVar variants found in the KIAA1522 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32741970-C-T		not specified	Uncertain significance (May 13, 2024)
1-32742019-C-A		not specified	Uncertain significance (May 10, 2023)
1-32742028-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-32742091-G-T		not specified	Uncertain significance (Mar 22, 2023)
1-32742099-A-G		not specified	Uncertain significance (Apr 05, 2023)
1-32742100-A-C		not specified	Uncertain significance (Apr 05, 2023)
1-32742133-C-T		not specified	Uncertain significance (Sep 12, 2023)
1-32742150-G-T		not specified	Uncertain significance (Feb 03, 2022)
1-32742153-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-32742166-A-G		not specified	Likely benign (Aug 02, 2023)
1-32767900-C-G		not specified	Uncertain significance (Aug 30, 2021)
1-32767922-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-32768086-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-32768112-A-G		not specified	Uncertain significance (May 15, 2024)
1-32768658-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-32768659-G-A		not specified	Uncertain significance (Jul 29, 2023)
1-32768692-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-32768739-G-A		not specified	Uncertain significance (May 25, 2022)
1-32768751-C-A		not specified	Uncertain significance (Feb 23, 2023)
1-32768755-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-32769668-C-A			Benign (Mar 29, 2018)
1-32769770-T-A		not specified	Uncertain significance (May 29, 2024)
1-32769916-G-C		not specified	Uncertain significance (Apr 08, 2024)
1-32769939-G-A		not specified	Uncertain significance (Feb 03, 2022)
1-32769942-C-T		not specified	Uncertain significance (Sep 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIAA1522	protein_coding	protein_coding	ENST00000401073	7	33086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0269	0.973	124735	0	61	124796	0.000244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0702	622	627	0.992	0.0000411	6790
Missense in Polyphen		120	108.23	1.1087		1231
Synonymous	-1.52	295	264	1.12	0.0000162	2597
Loss of Function	3.41	8	27.2	0.294	0.00000152	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000390
Ashkenazi Jewish	0.00277	0.00268
East Asian	0.0000594	0.0000556
Finnish	0.000103	0.0000928
European (Non-Finnish)	0.0000995	0.0000706
Middle Eastern	0.0000594	0.0000556
South Asian	0.000267	0.000261
Other	0.000504	0.000495

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0832

Intolerance Scores

• loftool: 0.429
• rvis_EVS: 0.43
• rvis_percentile_EVS: 77.33

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.474
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C77080

Gene ontology

• Biological process: cell differentiation