DOP1A

DOP1 leucine zipper like protein A

Basic information

Region (hg38): 6:83067666-83171350

Previous symbols: [ "KIAA1117", "DOPEY1" ]

Links

ENSG00000083097 ∙ NCBI:23033 ∙ OMIM:616823 ∙ HGNC:21194 ∙ Uniprot:Q5JWR5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DOP1A gene.

• not_specified (214 variants)
• not_provided (5 variants)
• PGM3-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DOP1A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015018.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			209	3		212
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	209	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DOP1A	protein_coding	protein_coding	ENST00000349129	37	103685

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000659	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.32	919	1.25e+3	0.736	0.0000611	16222
Missense in Polyphen		244	419.53	0.5816		5572
Synonymous	2.15	383	440	0.870	0.0000213	4708
Loss of Function	8.37	21	120	0.175	0.00000660	1453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000468	0.000459
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.000279	0.000272
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000241	0.000237
Middle Eastern	0.000279	0.000272
South Asian	0.000196	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in protein traffic between late Golgi and early endosomes. {ECO:0000250|UniProtKB:Q03921}.

Recessive Scores

• pRec: 0.0943

Intolerance Scores

• rvis_EVS: -1.05
• rvis_percentile_EVS: 7.62

Haploinsufficiency Scores

• pHI: 0.329
• hipred: Y
• hipred_score: 0.685
• ghis: 0.564

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Dop1a

Gene ontology

• Biological process: Golgi to endosome transport;protein transport
• Cellular component: Golgi membrane;endosome;trans-Golgi network;cytosol