KAAG1

kidney associated DCDC2 antisense RNA 1, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 6:24356903-24358285

Links

ENSG00000146049 ∙ NCBI:353219 ∙ OMIM:608211 ∙ HGNC:21031 ∙ Uniprot:Q9UBP8 ∙ 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 KAAG1 gene.

• Nephronophthisis 19;Isolated neonatal sclerosing cholangitis;Autosomal recessive nonsyndromic hearing loss 66 (1 variants)
• Isolated neonatal sclerosing cholangitis;Autosomal recessive nonsyndromic hearing loss 66 (1 variants)
• Dyslexia, susceptibility to, 2 (1 variants)
• Isolated neonatal sclerosing cholangitis (1 variants)
• not provided (1 variants)
• Nephronophthisis 19 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KAAG1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2	1	18	12	4	37
Total	2	1	18	12	4

Highest pathogenic variant AF is 0.00000657

Variants in KAAG1

This is a list of pathogenic ClinVar variants found in the KAAG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-24357379-G-A			Likely benign (Jun 16, 2018)
6-24357438-G-A		Isolated neonatal sclerosing cholangitis;Autosomal recessive nonsyndromic hearing loss 66	Likely benign (Feb 02, 2022)
6-24357457-CTTGAGTTTCTTGAAGGCTTCCTGGCCTCCAGCCACGTAATTGCCCCCGCTCTGGATCTGGTCTAGCTTCCG-C		Nephronophthisis 19	Likely pathogenic (-)
6-24357457-C-CT			Pathogenic (Sep 08, 2017)
6-24357473-G-T		Autosomal recessive nonsyndromic hearing loss 66 • Isolated neonatal sclerosing cholangitis;Nephronophthisis 19;Autosomal recessive nonsyndromic hearing loss 66 • DCDC2-related disorder	Uncertain significance (Dec 07, 2021)
6-24357493-G-A		DCDC2-related disorder	Likely benign (Aug 31, 2021)
6-24357504-C-G		DCDC2-related disorder	Uncertain significance (Oct 27, 2020)
6-24357512-A-G		Inborn genetic diseases	Uncertain significance (Feb 02, 2024)
6-24357519-C-G			Uncertain significance (Jan 14, 2020)
6-24357529-G-T		Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis • not specified • DCDC2-related disorder	Conflicting classifications of pathogenicity (Nov 19, 2023)
6-24357536-T-C			Uncertain significance (Nov 25, 2022)
6-24357542-G-T		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
6-24357545-C-T		DCDC2-related disorder	Likely benign (Feb 07, 2022)
6-24357568-G-A		Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis • not specified	Benign (Jan 31, 2024)
6-24357589-G-A		DCDC2-related disorder	Likely benign (Apr 18, 2022)
6-24357600-C-G		Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis;Nephronophthisis 19	Uncertain significance (Jun 17, 2024)
6-24357606-T-G			Uncertain significance (Apr 26, 2024)
6-24357607-C-G		Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis	Likely benign (Apr 14, 2023)
6-24357626-G-A		Isolated neonatal sclerosing cholangitis;Autosomal recessive nonsyndromic hearing loss 66	Uncertain significance (May 12, 2022)
6-24357626-GAC-G		Nephronophthisis 19 • Isolated neonatal sclerosing cholangitis • Dyslexia, susceptibility to, 2 • Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis • Autosomal recessive nonsyndromic hearing loss 66;Nephronophthisis 19;Isolated neonatal sclerosing cholangitis	Pathogenic (Mar 14, 2024)
6-24357634-C-T			Uncertain significance (Feb 03, 2020)
6-24357652-G-A		Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis	Likely benign (Oct 24, 2022)
6-24357658-C-T		Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis • not specified	Conflicting classifications of pathogenicity (Dec 17, 2023)
6-24357666-A-G		Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis	Uncertain significance (Aug 10, 2023)
6-24357675-C-G		Isolated neonatal sclerosing cholangitis	Likely pathogenic (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KAAG1	protein_coding	protein_coding	ENST00000274766	1	1382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.287	0.501	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	49	65.8	0.745	0.00000463	521
Missense in Polyphen		21	21.37	0.9827		157
Synonymous	1.92	18	31.8	0.566	0.00000254	198
Loss of Function	0.236	0	0.0646	0.00	2.66e-9	1

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0668

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.0378
• hipred: N
• hipred_score: 0.238
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: immune response
• Cellular component: cellular_component