SDAD1

protein-coding

SDA1 domain containing 1, the group of Armadillo like helical domain containing

Gene summary

Predicted to be involved in ribosomal large subunit biogenesis and ribosomal large subunit export from nucleus. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Located in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018115.4

Inheritance

—

ClinVar variants

U:108B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr4:75,940,950-75,990,962

External References & Databases

Ensembl (ENSG00000198301)

Transcript & Mutation Effects

hg38 • Region Span ~50.0 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 SDAD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018115.4. 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			3 clinvar	1 clinvar	2 clinvar	6
missense			102 clinvar	2 clinvar		104
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	108	3	2	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018115.4	RefSeq	NP_060585.2	22	MANE Select
ENST00000356260.10	Ensembl	ENSP00000348596.5	22	MANE Select
NM_001288983.2	RefSeq	NP_001275912.1	21	Standard
NM_001288984.2	RefSeq	NP_001275913.1	20	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
sdad1	Danio rerio	Structure: mandibular arch skeleton Quality: aplastic abnormal

Gene / Model

Organism

Observed Phenotype

sdad1

Danio rerio

Structure: mandibular arch skeleton

Quality: aplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ribosomal large subunit export from nucleus
actin cytoskeleton organization
ribosomal large subunit biogenesis

Molecular Function

molecular_function

Cellular Component

nucleus
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356260
Coding exons: 22
Length: 50013
Individuals with no LoFs: 125670
Homozygous LoFs: 0
Heterozygous LoFs: 78
Defined: 125748
p: 0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0327	362	360	1.00	0.0000181	4610
Missense (PolyPhen)		36	53.766	0.66956		801
Synonymous	0.183	122	125	0.979	0.00000618	1185
Loss of Function	1.31	36	45.5	0.791	0.00000259	521

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00074	0.00072	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for 60S pre-ribosomal subunits export to the cytoplasm. {ECO:0000250}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.942
RVIS EVS: -0.04
RVIS percentile EVS: 50.5

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.917

Gene Damage Prediction

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