KNDC1

kinase non-catalytic C-lobe domain containing 1

Basic information

Region (hg38): 10:133160219-133226412

Previous symbols: [ "RASGEF2", "C10orf23" ]

Links

ENSG00000171798 ∙ NCBI:85442 ∙ OMIM:616237 ∙ HGNC:29374 ∙ Uniprot:Q76NI1 ∙ 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 KNDC1 gene.

• not_specified (309 variants)
• not_provided (19 variants)
• Breast_ductal_adenocarcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KNDC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152643.8. 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				4	2	6
missense			283	29	7	319
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	284	33	9

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KNDC1	protein_coding	protein_coding	ENST00000304613	30	65966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00199	0.998	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.894	968	1.05e+3	0.922	0.0000704	11130
Missense in Polyphen		158	196.99	0.80206		2064
Synonymous	-0.0699	498	496	1.00	0.0000387	3618
Loss of Function	5.76	20	73.1	0.274	0.00000354	836

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000335	0.000332
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000994	0.0000924
European (Non-Finnish)	0.000148	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000107	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RAS-Guanine nucleotide exchange factor (GEF) that controls the negative regulation of neuronal dendrite growth by mediating a signaling pathway linking RAS and MAP2 (By similarity). May be involved in cellular senescence (PubMed:24788352). {ECO:0000250|UniProtKB:Q0KK55, ECO:0000269|PubMed:24788352}.

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.522
• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.86

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.372
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.155

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kndc1
• Phenotype: normal phenotype

Gene ontology

• Biological process: positive regulation of protein phosphorylation;small GTPase mediated signal transduction;biological_process;cerebellar granule cell differentiation;regulation of dendrite morphogenesis;regulation of dendrite development
• Cellular component: cellular_component;dendrite;guanyl-nucleotide exchange factor complex;neuronal cell body;perikaryon
• Molecular function: molecular_function;Ras guanyl-nucleotide exchange factor activity