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.

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.

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				3	2	5
missense			123	17	6	146
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1	1		2
Total	0	0	124	21	8

Variants in KNDC1

This is a list of pathogenic ClinVar variants found in the KNDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-133160487-C-A		not specified	Uncertain significance (May 18, 2022)
10-133167449-C-T			Likely benign (May 01, 2022)
10-133167477-C-T		not specified	Uncertain significance (May 23, 2023)
10-133167478-G-A		not specified	Likely benign (Jan 29, 2024)
10-133167492-G-T		not specified	Likely benign (Jun 07, 2024)
10-133167495-G-T		not specified	Uncertain significance (Jun 27, 2022)
10-133167525-G-A		not specified	Uncertain significance (Oct 16, 2023)
10-133167544-C-T		not specified	Uncertain significance (Nov 10, 2022)
10-133167555-G-A		not specified	Uncertain significance (Mar 26, 2024)
10-133168292-G-A		not specified	Uncertain significance (Aug 17, 2022)
10-133168448-C-T			Uncertain significance (Mar 01, 2024)
10-133183392-G-A		not specified	Uncertain significance (Oct 26, 2022)
10-133183470-G-A		not specified	Likely benign (Oct 12, 2022)
10-133183476-C-G		not specified	Uncertain significance (Sep 01, 2021)
10-133183477-G-A		not specified	Uncertain significance (Jun 28, 2023)
10-133185982-G-A		not specified	Uncertain significance (Jan 10, 2022)
10-133185994-C-T		not specified	Uncertain significance (Oct 06, 2022)
10-133185995-G-A		not specified	Uncertain significance (Oct 02, 2023)
10-133185995-G-T		not specified	Uncertain significance (Mar 30, 2024)
10-133186028-G-A		not specified	Likely benign (Apr 20, 2024)
10-133186042-G-A		not specified	Uncertain significance (Aug 22, 2023)
10-133186078-G-A		not specified	Likely benign (Jan 10, 2023)
10-133186078-G-C		not specified	Uncertain significance (Oct 14, 2023)
10-133186118-C-G		not specified	Uncertain significance (Oct 30, 2023)
10-133186204-G-A			Likely benign (Jul 01, 2024)

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