KCTD19

potassium channel tetramerization domain containing 19, the group of KCTD family

Basic information

Region (hg38): 16:67289428-67326760

Links

ENSG00000168676 ∙ NCBI:146212 ∙ OMIM:619943 ∙ HGNC:24753 ∙ Uniprot:Q17RG1 ∙ 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 KCTD19 gene.

• not_specified (99 variants)
• not_provided (6 variants)
• Cerebral_visual_impairment_and_intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001100915.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	2	4
missense		1	96	3	1	101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1		1
Total	0	1	96	6	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD19	protein_coding	protein_coding	ENST00000304372	16	37336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.07e-15	0.920	124516	1	294	124811	0.00118

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	432	514	0.840	0.0000280	6023
Missense in Polyphen		114	148.06	0.76995		1902
Synonymous	-0.0634	216	215	1.01	0.0000125	1852
Loss of Function	2.19	30	46.0	0.652	0.00000231	528

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00139
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.00217	0.00212
Finnish	0.00376	0.00372
European (Non-Finnish)	0.00105	0.00104
Middle Eastern	0.00217	0.00212
South Asian	0.000360	0.000360
Other	0.00133	0.00132

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.862
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.83

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.545
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd19

Gene ontology

• Biological process: protein homooligomerization