KAAG1

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

Basic information

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.

• not provided (17 variants)
• Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis (7 variants)
• Inborn genetic diseases (7 variants)
• Isolated neonatal sclerosing cholangitis;Autosomal recessive nonsyndromic hearing loss 66 (5 variants)
• not specified (2 variants)
• Isolated neonatal sclerosing cholangitis (2 variants)
• Autosomal recessive nonsyndromic hearing loss 66;Isolated neonatal sclerosing cholangitis;Nephronophthisis 19 (1 variants)
• Autosomal recessive nonsyndromic hearing loss 66;Nephronophthisis 19;Isolated neonatal sclerosing cholangitis (1 variants)
• Nephronophthisis 19;Isolated neonatal sclerosing cholangitis;Autosomal recessive nonsyndromic hearing loss 66 (1 variants)
• Dyslexia, susceptibility to, 2 (1 variants)
• Autosomal recessive nonsyndromic hearing loss 66 (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		17	8	4	31
Total	2	0	17	8	4

Highest pathogenic variant AF is 0.00000657

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