STARD9

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

Basic information

Region (hg38): 15:42575606-42720998

Links

ENSG00000159433 ∙ NCBI:57519 ∙ OMIM:614642 ∙ HGNC:19162 ∙ Uniprot:Q9P2P6 ∙ 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 STARD9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STARD9 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				16	11	27
missense			423	64	19	506
nonsense			5			5
start loss						0
frameshift			5	1		6
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1	1	1	3
non coding					2	2
Total	0	0	434	81	32

Variants in STARD9

This is a list of pathogenic ClinVar variants found in the STARD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-42575758-A-G		not specified	Uncertain significance (Apr 20, 2024)
15-42583368-A-G		not specified	Uncertain significance (May 03, 2023)
15-42585527-A-T		not specified	Uncertain significance (Jan 24, 2024)
15-42585561-A-G		STARD9-related disorder • not specified	Uncertain significance (Jul 06, 2021)
15-42585566-A-G		not specified	Likely benign (Mar 15, 2024)
15-42585609-A-G		not specified	Uncertain significance (Dec 13, 2023)
15-42634950-C-T		not specified	Uncertain significance (Jun 26, 2024)
15-42637928-C-T		not specified	Uncertain significance (Aug 21, 2024)
15-42637933-A-G		not specified	Uncertain significance (Feb 17, 2024)
15-42638042-A-G		not specified	Uncertain significance (Oct 06, 2023)
15-42638072-G-A		not specified	Uncertain significance (Jun 13, 2023)
15-42638713-T-C		not specified	Uncertain significance (Apr 08, 2022)
15-42638723-G-A		not specified	Uncertain significance (Oct 12, 2024)
15-42638762-C-G		not specified	Uncertain significance (Jul 13, 2021)
15-42638774-G-A		not specified	Uncertain significance (Feb 28, 2023)
15-42638784-G-A			Likely benign (May 02, 2018)
15-42638801-C-T		not specified	Uncertain significance (Aug 19, 2023)
15-42638810-A-C		not specified	Uncertain significance (Nov 10, 2024)
15-42651010-C-T		STARD9-related disorder	Likely benign (Jul 19, 2019)
15-42652566-G-A		not specified	Uncertain significance (Sep 26, 2024)
15-42652570-T-G		not specified	Uncertain significance (Apr 12, 2023)
15-42652576-C-A		not specified	Uncertain significance (Mar 29, 2023)
15-42652576-C-T		not specified	Uncertain significance (Oct 27, 2023)
15-42661174-A-G			Likely benign (Nov 01, 2022)
15-42661176-C-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STARD9	protein_coding	protein_coding	ENST00000290607	33	145323

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-38	1.00	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	2049	2.39e+3	0.856	0.000123	30591
Missense in 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

LoF frequencies by population

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

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.155

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.708

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stard9

Gene ontology

• Biological process: microtubule-based movement;spindle assembly
• Cellular component: nucleus;cytoplasm;centriole
• Molecular function: microtubule motor activity;ATP binding;microtubule binding;lipid binding