VPS13A

vacuolar protein sorting 13 homolog A, the group of bridge-like lipid transfer protein family

Basic information

Region (hg38): 9:77177445-77421537

Previous symbols: [ "CHAC" ]

Links

ENSG00000197969

∙ NCBI:23230 ∙ OMIM:605978 ∙ HGNC:1908 ∙ Uniprot:Q96RL7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

chorea-acanthocytosis (Strong), mode of inheritance: AR
chorea-acanthocytosis (Strong), mode of inheritance: AR
chorea-acanthocytosis (Supportive), mode of inheritance: AR
chorea-acanthocytosis (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Choreoacanthocytosis	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Hematologic; Musculoskeletal; Neurologic	4255726; 5677189; 4647152; 666266; 7081216; 7073550; 4026606; 1998879; 7936287; 8599563; 9382101; 10371080; 11381253; 11381254; 12404112; 15918062; 15824261; 17998451; 18584183; 18661137; 20301561; 21598378; 22038564; 23199253

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VPS13A gene.

not_provided (2893 variants)
Chorea-acanthocytosis (661 variants)
Inborn_genetic_diseases (349 variants)
not_specified (51 variants)
VPS13A-related_disorder (44 variants)
Abnormality_of_the_nervous_system (1 variants)
Vascular_dementia (1 variants)
See_cases (1 variants)
primray_hypomagnesemia_with_secondary_hypocalcemia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS13A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033305.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar		35 clinvar	1102 clinvar	16 clinvar	1154
missense	2 clinvar	5 clinvar	721 clinvar	71 clinvar	5 clinvar	804
nonsense	76 clinvar	29 clinvar				105
start loss		2				2
frameshift	161 clinvar	40 clinvar	1 clinvar			202
splice donor/acceptor (+/-2bp)	11 clinvar	99 clinvar	1 clinvar		1 clinvar	112
Total	251	175	758	1173	22

Highest pathogenic variant AF is 0.00008999148

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS13A	protein_coding	protein_coding	ENST00000360280	72	244189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.31e-22	1.00	125549	0	199	125748	0.000792

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	1408	1.61e+3	0.877	0.0000790	20931
Missense in Polyphen		381	522.91	0.72862		6900
Synonymous	0.127	540	544	0.993	0.0000275	5821
Loss of Function	7.34	68	172	0.396	0.00000884	2219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00160	0.00158
Ashkenazi Jewish	0.000697	0.000695
East Asian	0.00114	0.00114
Finnish	0.000562	0.000554
European (Non-Finnish)	0.000810	0.000800
Middle Eastern	0.00114	0.00114
South Asian	0.000688	0.000686
Other	0.000985	0.000978

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in the control of protein cycling through the trans-Golgi network to early and late endosomes, lysosomes and plasma membrane.;

Recessive Scores

pRec: 0.232

Intolerance Scores

loftool: 0.900
rvis_EVS: -1.85
rvis_percentile_EVS: 2.03

Haploinsufficiency Scores

pHI: 0.153
hipred: N
hipred_score: 0.414
ghis: 0.536

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.436

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Vps13a
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype;

Gene ontology

Biological process: protein targeting to vacuole;Golgi to endosome transport;autophagy;nervous system development;locomotory behavior;protein localization;social behavior;protein retention in Golgi apparatus
Cellular component: cytosol;extrinsic component of membrane;dense core granule
Molecular function: protein binding