DISP3

dispatched RND transporter family member 3, the group of Dispatched RND transporter family

Basic information

Region (hg38): 1:11479154-11537551

Previous symbols: [ "PTCHD2" ]

Links

ENSG00000204624 ∙ NCBI:57540 ∙ OMIM:611251 ∙ HGNC:29251 ∙ Uniprot:Q9P2K9 ∙ 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 DISP3 gene.

• not provided (9 variants)
• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DISP3 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
missense			9	1	4	14
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	10	1	5

Variants in DISP3

This is a list of pathogenic ClinVar variants found in the DISP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-11501000-C-T		DISP3-related disorder	Benign (Sep 05, 2019)
1-11501107-G-A		DISP3-related disorder	Benign (Oct 30, 2019)
1-11501113-G-A		not specified	Uncertain significance (Oct 05, 2021)
1-11501143-C-G		DISP3-related disorder	Benign (Jun 13, 2019)
1-11501200-A-G		DISP3-related disorder	Benign (Dec 22, 2020)
1-11501489-G-A		DISP3-related disorder	Likely benign (Jan 08, 2020)
1-11501536-G-A		DISP3-related disorder	Benign (Oct 17, 2019)
1-11501543-G-T		DISP3-related disorder	Benign (Aug 09, 2019)
1-11501577-C-T		DISP3-related disorder	Likely benign (Oct 28, 2019)
1-11501625-G-T		not specified	Uncertain significance (Oct 05, 2021)
1-11501635-G-T			Benign (Dec 31, 2019)
1-11501706-C-T		DISP3-related disorder	Likely benign (Jun 14, 2019)
1-11501874-C-T		DISP3-related disorder	Likely benign (Jul 19, 2019)
1-11501880-C-T		DISP3-related disorder	Benign (Oct 30, 2019)
1-11502856-C-T		DISP3-related disorder	Benign (Oct 30, 2019)
1-11516008-C-T		DISP3-related disorder	Benign (Jul 23, 2019)
1-11516037-G-A			Likely benign (May 01, 2023)
1-11516110-C-T		DISP3-related disorder	Likely benign (May 24, 2019)
1-11516149-C-T			Benign (Feb 25, 2018)
1-11516166-G-A		DISP3-related disorder	Likely benign (Dec 21, 2020)
1-11517564-CCT-C			Uncertain significance (Dec 30, 2021)
1-11519413-G-A		DISP3-related disorder	Benign (Oct 16, 2019)
1-11519447-G-C		DISP3-related disorder	Benign (Oct 21, 2019)
1-11519451-C-T		DISP3-related disorder	Likely benign (Aug 02, 2019)
1-11519738-C-T		DISP3-related disorder	Likely benign (Apr 30, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DISP3	protein_coding	protein_coding	ENST00000294484	20	58419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.63e-8	1.00	124934	0	76	125010	0.000304

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	772	900	0.858	0.0000607	8911
Missense in Polyphen		252	365.29	0.68986		3662
Synonymous	0.803	390	411	0.950	0.0000300	2962
Loss of Function	4.44	24	61.6	0.390	0.00000314	621

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000918	0.000905
Ashkenazi Jewish	0.000106	0.0000993
East Asian	0.000225	0.000223
Finnish	0.000283	0.000278
European (Non-Finnish)	0.000282	0.000265
Middle Eastern	0.000225	0.000223
South Asian	0.000334	0.000327
Other	0.000175	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in neuronal proliferation and differentiation (PubMed:25281927). Plays a role in the accumulation of cellular cholesterol (By similarity). Involved in intracellular lipid droplet formation (PubMed:25281927). May contribute to cholesterol homeostasis in neuronal cells (By similarity). {ECO:0000250|UniProtKB:B9U3F2, ECO:0000269|PubMed:25281927}.
• Pathway: HH-Core (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.700
• ghis: 0.544

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Disp3

Gene ontology

• Biological process: smoothened signaling pathway;cholesterol metabolic process;regulation of lipid transport;cholesterol homeostasis;negative regulation of neuron differentiation;positive regulation of lipid metabolic process;positive regulation of neural precursor cell proliferation
• Cellular component: cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;cytoplasmic vesicle membrane;nuclear membrane
• Molecular function: molecular_function