STARD13

StAR related lipid transfer domain containing 13, the group of StAR related lipid transfer domain containing|Rho GTPase activating proteins

Basic information

Region (hg38): 13:33103136-33350630

Previous symbols: [ "LINC00464" ]

Links

ENSG00000133121 ∙ NCBI:90627 ∙ OMIM:609866 ∙ HGNC:19164 ∙ Uniprot:Q9Y3M8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STARD13 gene.

• Inborn genetic diseases (60 variants)
• not provided (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STARD13 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				5	9	14
missense			58	6		64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	11	9

Variants in STARD13

This is a list of pathogenic ClinVar variants found in the STARD13 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-33105661-C-T		not specified	Uncertain significance (May 30, 2023)
13-33106767-A-G		not specified	Uncertain significance (Apr 18, 2023)
13-33106808-C-T			Benign/Likely benign (Jul 01, 2022)
13-33106824-T-C		not specified	Uncertain significance (Feb 27, 2023)
13-33106839-A-T			Likely benign (Apr 16, 2018)
13-33106862-C-G		not specified	Uncertain significance (May 18, 2023)
13-33109888-T-G		not specified	Uncertain significance (Apr 13, 2022)
13-33109898-G-A			Likely benign (Mar 30, 2018)
13-33109901-G-A		not specified	Uncertain significance (Feb 27, 2024)
13-33109903-G-A		not specified	Uncertain significance (Dec 01, 2022)
13-33109903-G-T		not specified	Uncertain significance (Jul 31, 2023)
13-33109945-C-T		not specified	Likely benign (May 31, 2023)
13-33109952-G-C		not specified	Uncertain significance (Aug 15, 2023)
13-33109985-C-T		not specified	Uncertain significance (Nov 02, 2023)
13-33109999-C-T		not specified	Uncertain significance (Jan 30, 2024)
13-33110031-G-A			Benign (Apr 20, 2018)
13-33110725-C-T			Benign (May 30, 2018)
13-33110753-G-A		not specified	Uncertain significance (Dec 21, 2022)
13-33112724-G-A		not specified	Uncertain significance (Jan 29, 2024)
13-33112790-A-G		not specified	Uncertain significance (Sep 01, 2021)
13-33112794-G-A		not specified	Uncertain significance (Jun 03, 2022)
13-33112830-C-G		not specified	Uncertain significance (Jan 04, 2024)
13-33112903-G-A			Benign (Apr 09, 2018)
13-33112920-C-G		not specified	Uncertain significance (Mar 01, 2024)
13-33118127-C-T		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STARD13	protein_coding	protein_coding	ENST00000336934	14	247496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.35e-8	1.00	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.255	624	642	0.972	0.0000378	7331
Missense in Polyphen		170	214.55	0.79236		2553
Synonymous	-2.15	306	262	1.17	0.0000170	2176
Loss of Function	3.53	21	47.2	0.445	0.00000260	529

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000546	0.000546
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000189	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.000328	0.000327
Other	0.000350	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells. {ECO:0000269|PubMed:14697242, ECO:0000269|PubMed:16217026}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.773
• rvis_EVS: -1.27
• rvis_percentile_EVS: 5.21

Haploinsufficiency Scores

• pHI: 0.551
• hipred: Y
• hipred_score: 0.545
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stard13
• Phenotype: neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;endothelial cell migration;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;negative regulation of cell migration involved in sprouting angiogenesis;endothelial tube lumen extension
• Cellular component: lipid droplet;cytosol;mitochondrial membrane
• Molecular function: GTPase activator activity;protein binding;lipid binding