DOLPP1

dolichyldiphosphatase 1, the group of Lipid phosphatases

Basic information

Region (hg38): 9:129081111-129090438

Links

ENSG00000167130 ∙ NCBI:57171 ∙ OMIM:614516 ∙ HGNC:29565 ∙ Uniprot:Q86YN1 ∙ 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 DOLPP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DOLPP1 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						0
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in DOLPP1

This is a list of pathogenic ClinVar variants found in the DOLPP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-129081147-C-G		not specified	Uncertain significance (Dec 20, 2023)
9-129084682-C-T		not specified	Uncertain significance (Feb 06, 2024)
9-129085078-A-C		not specified	Uncertain significance (Feb 06, 2024)
9-129085285-C-T		not specified	Uncertain significance (Jan 16, 2025)
9-129085588-G-A		not specified	Likely benign (Dec 29, 2024)
9-129085612-A-G		not specified	Uncertain significance (Jan 21, 2025)
9-129086194-G-A		not specified	Likely benign (Mar 31, 2024)
9-129086233-G-T		not specified	Uncertain significance (Jun 24, 2022)
9-129086246-T-G		not specified	Uncertain significance (Feb 16, 2023)
9-129086758-G-A		not specified	Uncertain significance (Nov 21, 2022)
9-129088975-A-G		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DOLPP1	protein_coding	protein_coding	ENST00000372546	8	9339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.175	0.823	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	86	146	0.590	0.00000859	1524
Missense in Polyphen		16	47.348	0.33793		565
Synonymous	0.235	61	63.4	0.962	0.00000411	485
Loss of Function	2.64	4	15.1	0.266	7.29e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for efficient N-glycosylation. Necessary for maintaining optimal levels of dolichol-linked oligosaccharides. Hydrolyzes dolichyl pyrophosphate at a very high rate and dolichyl monophosphate at a much lower rate. Does not act on phosphatidate (By similarity). {ECO:0000250|UniProtKB:Q9JMF7}.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Synthesis of Dolichyl-phosphate;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.167
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.571
• hipred: Y
• hipred_score: 0.673
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dolpp1

Gene ontology

• Biological process: protein N-linked glycosylation;dolichyl diphosphate biosynthetic process;lipid biosynthetic process
• Cellular component: endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane
• Molecular function: dolichyldiphosphatase activity