RCSD1

protein-coding

RCSD domain containing 1

Gene summary

Enables actin filament binding activity. Involved in cellular hyperosmotic response. Predicted to be located in actin filament. Predicted to be part of WASH complex. Predicted to be active in early endosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_052862.4

Inheritance

—

ClinVar variants

U:76B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr1:167,630,093-167,708,696

External References & Databases

Ensembl (ENSG00000198771)

Transcript & Mutation Effects

hg38 • Region Span ~78.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RCSD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 75

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052862.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			73 clinvar	4 clinvar		77
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	4	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052862.4	RefSeq	NP_443094.3	7	MANE Select
ENST00000367854.8	Ensembl	ENSP00000356828.3	7	MANE Select
NM_001322923.2	RefSeq	NP_001309852.1	6	Standard
NM_001322924.2	RefSeq	NP_001309853.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

skeletal muscle contraction
cellular hyperosmotic response

Molecular Function

actin filament binding

Cellular Component

actin filament

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367854
Coding exons: 7
Length: 76157
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125747
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.443	249	230	1.08	0.0000123	2661
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.335

Gene Damage Prediction

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