RCCD1

RCC1 domain containing 1

Basic information

Region (hg38): 15:90954881-90963125

Links

ENSG00000166965 ∙ NCBI:91433 ∙ OMIM:617997 ∙ HGNC:30457 ∙ Uniprot:A6NED2 ∙ 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 RCCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCCD1 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	3
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	3

Variants in RCCD1

This is a list of pathogenic ClinVar variants found in the RCCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-90956760-G-C		not specified	Uncertain significance (Feb 10, 2022)
15-90956764-C-A		not specified	Uncertain significance (Jul 05, 2023)
15-90956766-G-C		not specified	Uncertain significance (Mar 20, 2023)
15-90956770-C-G		not specified	Uncertain significance (Jul 25, 2023)
15-90956827-C-A		not specified	Uncertain significance (May 09, 2023)
15-90957157-G-A		not specified	Uncertain significance (Apr 12, 2024)
15-90957205-C-T		not specified	Uncertain significance (Nov 09, 2021)
15-90957231-A-C		not specified	Uncertain significance (Jun 21, 2022)
15-90957238-G-A		not specified	Uncertain significance (Jul 20, 2021)
15-90957245-C-A		not specified	Uncertain significance (Jun 29, 2023)
15-90957296-C-T		not specified	Uncertain significance (Aug 30, 2021)
15-90957302-C-T		not specified	Uncertain significance (Aug 13, 2021)
15-90957324-C-T			Benign (Mar 29, 2018)
15-90957364-G-A		not specified	Uncertain significance (Apr 12, 2023)
15-90957391-C-T		not specified	Uncertain significance (Jul 12, 2022)
15-90957403-C-T		not specified	Uncertain significance (Jun 29, 2023)
15-90957432-G-C		not specified	Uncertain significance (Jun 13, 2022)
15-90957635-G-A		not specified	Uncertain significance (May 03, 2023)
15-90957647-C-A		not specified	Uncertain significance (May 08, 2023)
15-90957707-C-T		not specified	Uncertain significance (Jun 03, 2024)
15-90959965-C-T			Benign (Dec 31, 2019)
15-90960356-G-C		not specified	Uncertain significance (Mar 01, 2024)
15-90960369-G-A		not specified	Uncertain significance (Jul 26, 2022)
15-90960484-C-T		not specified	Uncertain significance (May 31, 2023)
15-90961650-A-G		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCCD1	protein_coding	protein_coding	ENST00000394258	7	8250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.27e-11	0.0461	125685	0	62	125747	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.209	174	182	0.956	0.00000976	2321
Missense in Polyphen		72	71.396	1.0085		851
Synonymous	-0.677	92	84.1	1.09	0.00000489	816
Loss of Function	-0.0539	16	15.8	1.01	8.70e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000284	0.000281
Middle Eastern	0.000327	0.000326
South Asian	0.000461	0.000457
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a coregulator of KDM8 to promote histone demethylase activity on di- and trimethylated 'Lys-36' (H3K36me2/me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8 (PubMed:24981860). Possibly together with KDM8, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha- tubulin deacetylation and cytoskeletal microtubule stability and thereby promoting cell migration and TGF-beta-induced epithelial to mesenchymal transition (EMT), potentially through the inhibition of KDM8 (PubMed:28455245). {ECO:0000269|PubMed:24981860, ECO:0000269|PubMed:28455245}.

Recessive Scores

• pRec: 0.0950

Haploinsufficiency Scores

• pHI: 0.0325
• hipred: N
• hipred_score: 0.180
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rccd1

Gene ontology

• Biological process: chromatin organization
• Cellular component: chromosome;cytosol;plasma membrane