RCSD1

RCSD domain containing 1

Basic information

Region (hg38): 1:167630092-167708696

Links

ENSG00000198771 ∙ NCBI:92241 ∙ OMIM:610579 ∙ HGNC:28310 ∙ Uniprot:Q6JBY9 ∙ 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 RCSD1 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCSD1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in RCSD1

This is a list of pathogenic ClinVar variants found in the RCSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-167683939-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-167683985-C-T		not specified	Uncertain significance (Aug 31, 2023)
1-167685425-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-167685446-G-A		not specified	Uncertain significance (Dec 21, 2022)
1-167685467-C-A		not specified	Uncertain significance (Dec 20, 2023)
1-167685478-C-G		not specified	Uncertain significance (Jan 03, 2024)
1-167685478-C-T		not specified	Uncertain significance (Jun 30, 2023)
1-167690071-A-T		not specified	Uncertain significance (Nov 17, 2022)
1-167694174-T-C		not specified	Uncertain significance (Nov 06, 2023)
1-167694220-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-167694261-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-167694266-G-T		not specified	Uncertain significance (Mar 02, 2023)
1-167694268-C-A		not specified	Uncertain significance (Jun 02, 2023)
1-167697175-T-G		not specified	Uncertain significance (Feb 10, 2023)
1-167697192-G-T		not specified	Uncertain significance (Aug 16, 2021)
1-167697198-T-C		not specified	Likely benign (Oct 20, 2021)
1-167697244-T-G		not specified	Uncertain significance (Feb 17, 2022)
1-167697280-C-T		not specified	Uncertain significance (May 09, 2022)
1-167697390-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-167697421-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-167697424-G-A		not specified	Likely benign (Oct 27, 2023)
1-167697475-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-167697586-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-167697697-G-A		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCSD1	protein_coding	protein_coding	ENST00000367854	7	76157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0362	0.962	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.443	249	230	1.08	0.0000123	2661
Missense in Polyphen		91	84.106	1.082		913
Synonymous	0.189	95	97.4	0.976	0.00000589	843
Loss of Function	2.80	6	19.2	0.312	0.00000112	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stress-induced phosphorylation of CAPZIP may regulate the ability of F-actin-capping protein to remodel actin filament assembly. {ECO:0000269|PubMed:15850461}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.655
• rvis_EVS: 0
• rvis_percentile_EVS: 54.03

Haploinsufficiency Scores

• pHI: 0.315
• hipred: N
• hipred_score: 0.280
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.335

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcsd1

Gene ontology

• Biological process: skeletal muscle contraction;cellular hyperosmotic response
• Cellular component: actin filament
• Molecular function: actin filament binding