RUBCNL

rubicon like autophagy enhancer, the group of PIK3C3 complex subunits

Basic information

Region (hg38): 13:46334681-46438190

Previous symbols: [ "C13orf18", "KIAA0226L" ]

Links

ENSG00000102445 ∙ NCBI:80183 ∙ OMIM:620175 ∙ HGNC:20420 ∙ Uniprot:Q9H714 ∙ 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 RUBCNL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUBCNL 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			3		1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	1

Variants in RUBCNL

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

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

Position	Type	Phenotype	Significance	ClinVar
13-46345485-T-A		not specified	Uncertain significance (Jul 06, 2021)
13-46359610-G-A		Malignant tumor of prostate	Uncertain significance (-)
13-46368077-G-A		not specified	Uncertain significance (Aug 23, 2021)
13-46368135-G-C		not specified	Uncertain significance (Jul 06, 2021)
13-46371941-C-G			Benign (Jul 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUBCNL	protein_coding	protein_coding	ENST00000429979	13	96187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.36e-18	0.0109	125452	1	198	125651	0.000792

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	332	346	0.960	0.0000180	4330
Missense in Polyphen		74	87.425	0.84644		1164
Synonymous	0.318	134	139	0.966	0.00000798	1261
Loss of Function	0.374	28	30.2	0.927	0.00000144	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000526	0.000496
Ashkenazi Jewish	0.000399	0.000397
East Asian	0.00261	0.00190
Finnish	0.00430	0.00426
European (Non-Finnish)	0.000469	0.000414
Middle Eastern	0.00261	0.00190
South Asian	0.000108	0.0000980
Other	0.000819	0.000816

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a tumor suppressor. {ECO:0000269|PubMed:23522960}.

Recessive Scores

• pRec: 0.0693

Intolerance Scores

• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.87

Haploinsufficiency Scores

• pHI: 0.0468
• hipred: N
• hipred_score: 0.352
• ghis: 0.435

Mouse Genome Informatics

• Gene name: Rubcnl