STARD3

StAR related lipid transfer domain containing 3, the group of StAR related lipid transfer domain containing

Basic information

Region (hg38): 17:39637089-39664201

Links

ENSG00000131748 ∙ ∙ OMIM:607048 ∙ HGNC:17579 ∙ Uniprot:Q14849 ∙ 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 STARD3 gene.

• Inborn genetic diseases (20 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STARD3 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				1	1	2
missense			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	1

Variants in STARD3

This is a list of pathogenic ClinVar variants found in the STARD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-39653551-A-T		not specified	Uncertain significance (Nov 21, 2022)
17-39653570-G-T		not specified	Uncertain significance (Mar 29, 2022)
17-39653571-C-G		not specified	Uncertain significance (Sep 20, 2023)
17-39653572-G-A		not specified	Uncertain significance (Sep 17, 2021)
17-39653673-G-A		not specified	Uncertain significance (Nov 02, 2023)
17-39653683-G-T		not specified	Uncertain significance (Aug 08, 2022)
17-39653708-C-T			Likely benign (Apr 01, 2022)
17-39657023-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-39657062-A-G		not specified	Uncertain significance (May 17, 2023)
17-39657081-T-C		not specified	Uncertain significance (Jun 02, 2023)
17-39657787-T-C		not specified	Uncertain significance (Jun 22, 2023)
17-39657978-G-A		not specified	Likely benign (Jan 31, 2024)
17-39658439-C-T		not specified	Uncertain significance (Jul 30, 2023)
17-39658444-G-A		not specified	Uncertain significance (Jun 13, 2023)
17-39658466-T-G		not specified	Uncertain significance (Jun 21, 2021)
17-39658494-C-T		not specified	Likely benign (Jan 17, 2024)
17-39658733-G-A		not specified	Uncertain significance (Sep 14, 2022)
17-39658771-C-T			Benign (Jan 01, 2023)
17-39659473-A-G		not specified	Likely benign (Apr 18, 2023)
17-39659495-C-T		not specified	Likely benign (Feb 10, 2022)
17-39660438-T-C		not specified	Uncertain significance (Dec 02, 2022)
17-39660443-T-C		not specified	Uncertain significance (Jan 29, 2024)
17-39660458-G-A		not specified	Uncertain significance (Oct 06, 2023)
17-39660474-T-C		not specified	Uncertain significance (Jan 29, 2024)
17-39660852-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STARD3	protein_coding	protein_coding	ENST00000336308	14	26420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000789	0.999	125719	0	27	125746	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	241	284	0.849	0.0000190	2849
Missense in Polyphen		87	99.612	0.87339		992
Synonymous	-0.767	128	117	1.09	0.00000761	911
Loss of Function	2.95	12	29.2	0.411	0.00000167	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sterol-binding protein that mediates cholesterol transport from the endoplasmic reticulum to endosomes (PubMed:11053434, PubMed:15930133, PubMed:22514632, PubMed:28377464). Creates contact site between the endoplasmic reticulum and late endosomes: localizes to late endosome membranes and contacts the endoplasmic reticulum via interaction with VAPA and VAPB (PubMed:24105263, PubMed:28377464). Acts as a lipid transfer protein that redirects sterol to the endosome at the expense of the cell membrane and favors membrane formation inside endosomes (PubMed:28377464). May also mediate cholesterol transport between other membranes, such as mitochondria membrane or cell membrane (PubMed:12070139, PubMed:19965586). However, such results need additional experimental evidences; probably mainly mediates cholesterol transport from the endoplasmic reticulum to endosomes (PubMed:28377464). Does not activate transcriptional cholesterol sensing (PubMed:28377464). Able to bind other lipids, such as lutein, a xanthophyll carotenoids that form the macular pigment of the retina (PubMed:21322544). {ECO:0000269|PubMed:11053434, ECO:0000269|PubMed:12070139, ECO:0000269|PubMed:15930133, ECO:0000269|PubMed:19965586, ECO:0000269|PubMed:21322544, ECO:0000269|PubMed:22514632, ECO:0000269|PubMed:24105263, ECO:0000269|PubMed:28377464}.
• Pathway: Cholesterol metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Pregnenolone biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Bile acid biosynthesis;C21-steroid hormone biosynthesis and metabolism;Steroid hormones (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.0559
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.17

Haploinsufficiency Scores

• pHI: 0.141
• hipred: Y
• hipred_score: 0.554
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stard3
• Phenotype: homeostasis/metabolism phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: lipid metabolic process;C21-steroid hormone biosynthetic process;progesterone biosynthetic process;mitochondrial transport;steroid metabolic process;cholesterol metabolic process;cholesterol transport;vesicle tethering to endoplasmic reticulum
• Cellular component: cytoplasm;mitochondrion;lysosomal membrane;endoplasmic reticulum membrane;cytosol;integral component of membrane;late endosome membrane;organelle membrane contact site
• Molecular function: protein binding;cholesterol binding;cholesterol transporter activity;protein homodimerization activity