DISP1

dispatched RND transporter family member 1, the group of Dispatched RND transporter family

Basic information

Region (hg38): 1:222815022-223005995

Links

ENSG00000154309 ∙ NCBI:84976 ∙ OMIM:607502 ∙ HGNC:19711 ∙ Uniprot:Q96F81 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• holoprosencephaly 5 (Limited), mode of inheritance: AD
• holoprosencephaly (Supportive), mode of inheritance: AR
• holoprosencephaly (Limited), mode of inheritance: Semidominant
• holoprosencephaly (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DISP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DISP1 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				65	11	76
missense			170	12	11	193
nonsense			11			11
start loss						0
frameshift			8			8
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region				1	2	3
non coding			1	10	13	24
Total	0	0	192	87	35

Variants in DISP1

This is a list of pathogenic ClinVar variants found in the DISP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-222942528-G-A			Likely benign (Jan 28, 2020)
1-222942767-C-T			Benign (Nov 10, 2018)
1-222942830-A-G		not specified	Uncertain significance (Jan 15, 2024)
1-222942856-GGTTC-G			Uncertain significance (Mar 20, 2023)
1-222942874-C-T			Likely benign (Aug 09, 2018)
1-222942875-A-T			Uncertain significance (May 09, 2022)
1-222942877-C-T		DISP1-related disorder	Likely benign (May 17, 2021)
1-222942879-C-T			Uncertain significance (Dec 11, 2023)
1-222942885-G-A			Uncertain significance (May 11, 2022)
1-222942898-G-A			Benign (Jan 29, 2024)
1-222942904-C-G		DISP1-related disorder	Likely benign (Mar 23, 2023)
1-222942912-C-T			Uncertain significance (Apr 28, 2016)
1-222943002-G-T			Uncertain significance (Feb 14, 2023)
1-222943005-C-T		not specified	Uncertain significance (Dec 30, 2023)
1-222943006-G-A		DISP1-related disorder	Likely benign (Aug 16, 2022)
1-222943009-C-G		DISP1-related disorder	Benign (Feb 08, 2023)
1-222943036-C-A		not specified	Uncertain significance (Apr 18, 2023)
1-222943052-A-C			Uncertain significance (Nov 23, 2022)
1-222943098-C-G			Likely benign (Jan 18, 2024)
1-222943104-A-G		not specified	Uncertain significance (Jun 13, 2024)
1-222943130-G-A		not specified	Benign (Jan 29, 2024)
1-222943130-GAG-AAT			Benign (Nov 29, 2023)
1-222943132-G-T		not specified	Benign (Jan 29, 2024)
1-222943145-G-A			Uncertain significance (Apr 05, 2023)
1-222943149-C-T			Uncertain significance (Nov 30, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DISP1	protein_coding	protein_coding	ENST00000284476	7	190932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.86e-8	1.00	125655	0	93	125748	0.000370

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.930	730	804	0.908	0.0000437	10177
Missense in Polyphen		137	212.13	0.64584		2729
Synonymous	-0.563	325	312	1.04	0.0000192	2886
Loss of Function	3.87	21	50.7	0.414	0.00000266	640

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00157
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000326	0.000326
Finnish	0.0000924	0.0000462
European (Non-Finnish)	0.000309	0.000299
Middle Eastern	0.000326	0.000326
South Asian	0.000502	0.000490
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in hedgehog (Hh) signaling. Regulates the release and extracellular accumulation of cholesterol-modified hedgehog proteins and is hence required for effective production of the Hh signal (By similarity). Synergizes with SCUBE2 to cause a increase in SHH secretion (PubMed:22902404). {ECO:0000250|UniProtKB:Q3TDN0, ECO:0000269|PubMed:22902404}.
• Pathway: HH-Core;Signaling events mediated by the Hedgehog family (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.0629
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.78

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.492
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Disp1
• Phenotype: craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; vision/eye phenotype; digestive/alimentary 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); limbs/digits/tail phenotype; skeleton phenotype; respiratory system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: disp1
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: patched ligand maturation;determination of left/right symmetry;embryonic pattern specification;dorsal/ventral pattern formation;peptide transport;regulation of protein secretion;diaphragm development;protein homotrimerization
• Cellular component: integral component of membrane;basolateral plasma membrane
• Molecular function: protein binding;peptide transmembrane transporter activity