STARD9

protein-coding

StAR related lipid transfer domain containing 9, the group of StAR related lipid transfer domain containing|Kinesins

Gene summary

Enables microtubule binding activity and microtubule motor activity. Involved in spindle assembly. Located in centriole; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020759.3

Inheritance

—

ClinVar variants

U:786B:171

Top phenotype

STARD9-related disorder

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr15:42,575,606-42,720,998

External References & Databases

Ensembl (ENSG00000159433)

Transcript & Mutation Effects

hg38 • Region Span ~145.4 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 STARD9 variants in ClinVar

9 Conditions Cataloged

not specifiedTotal: 839

not providedTotal: 97

STARD9-related disorderTotal: 53

See casesTotal: 2

Autism spectrum disorderTotal: 1

SeizureTotal: 1

Global developmental delayTotal: 1

STARD9-related intellectual disabilities with blindnessTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020759.3. 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				37 clinvar	10 clinvar	47
missense			771 clinvar	101 clinvar	22 clinvar	894
nonsense			6 clinvar			6
start loss						0
frameshift			7 clinvar	1 clinvar		8
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	786	139	32	957

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020759.3	RefSeq	NP_065810.2	33	MANE Select
ENST00000290607.12	Ensembl	ENSP00000290607.7	33	MANE Select
ENST00000562619.1	Ensembl	ENSP00000454648.1	2	Standard
ENST00000569419.1	Ensembl	ENSP00000454594.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule-based movement
spindle assembly

Molecular Function

microtubule motor activity
ATP binding
microtubule binding
lipid binding

Cellular Component

nucleus
cytoplasm
centriole

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290607
Coding exons: 33
Length: 145323
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.50	2049	2.39e+3	0.856	0.000123	30591
Missense (PolyPhen)		431	534.85	0.80583		7628
Synonymous	3.47	801	936	0.856	0.0000492	9443
Loss of Function	5.73	92	173	0.531	0.00000929	2105

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Microtubule-dependent motor protein required for spindle pole assembly during mitosis. Required to stabilize the pericentriolar material (PCM). {ECO:0000269|PubMed:22153075}.;

Recessive Scores

pRec: 0.0819

Intolerance Scores

RVIS EVS: 7.31
RVIS percentile EVS: 99.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.708

Gene Damage Prediction

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