STARD13

protein-coding

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

Gene summary

This gene encodes a protein which contains an N-terminal sterile alpha motif (SAM) for protein-protein interactions, followed by an ATP/GTP-binding motif, a GTPase-activating protein (GAP) domain, and a C-terminal STAR-related lipid transfer (START) domain. It may be involved in regulation of cytoskeletal reorganization, cell proliferation, and cell motility, and acts as a tumor suppressor in hepatoma cells. The gene is located in a region of chromosome 13 that is associated with loss of heterozygosity in hepatocellular carcinomas. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

Previous symbols:

LINC00464

MANE transcript

NM_178006.4

Inheritance

—

ClinVar variants

U:152B:23

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr13:33,103,137-33,350,630

External References & Databases

Ensembl (ENSG00000133121)

Transcript & Mutation Effects

hg38 • Region Span ~247.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STARD13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 150

not providedTotal: 19

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178006.4. 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	6 clinvar	9 clinvar	18
missense			149 clinvar	8 clinvar		157
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	152	14	9	175

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178006.4	RefSeq	NP_821074.1	14	MANE Select
ENST00000336934.10	Ensembl	ENSP00000338785.4	14	MANE Select
NM_001243466.2	RefSeq	NP_001230395.1	8	Standard
NM_001243474.2	RefSeq	NP_001230403.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Rho GTPase cycle
Signaling by Rho GTPases

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

Molecular Function

GTPase activator activity
protein binding
lipid binding

Cellular Component

lipid droplet
cytosol
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336934
Coding exons: 14
Length: 247496
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125748
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.255	624	642	0.972	0.0000378	7331
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00033	0.00033	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.773
RVIS EVS: -1.27
RVIS percentile EVS: 5.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.895

Gene Damage Prediction

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