LDOC1

LDOC1 regulator of NFKB signaling, the group of Retrotransposon Gag like

Basic information

Region (hg38): X:141111605-141177129

Previous symbols: [ "BCUR1" ]

Links

ENSG00000182195 ∙ NCBI:23641 ∙ OMIM:300402 ∙ HGNC:6548 ∙ Uniprot:O95751 ∙ 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 LDOC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDOC1 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			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	0

Variants in LDOC1

This is a list of pathogenic ClinVar variants found in the LDOC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-141176602-T-G		not specified	Likely benign (Dec 15, 2023)
X-141176894-T-C		not specified	Uncertain significance (Nov 08, 2022)
X-141176943-T-G		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDOC1	protein_coding	protein_coding	ENST00000370526	1	1377

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.524	0.418	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	27	61.5	0.439	0.00000402	973
Missense in Polyphen		7	17.934	0.39031		307
Synonymous	0.272	26	27.8	0.934	0.00000192	282
Loss of Function	1.36	0	2.16	0.00	1.40e-7	27

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have an important role in the development and/or progression of some cancers.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.365
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldoc1

Gene ontology

• Biological process: maternal placenta development;negative regulation of cell population proliferation;maternal process involved in parturition;cellular response to lipopolysaccharide;cellular response to muramyl dipeptide;regulation of growth hormone activity
• Cellular component: nucleus;nucleolus
• Molecular function: protein binding