CEP112

centrosomal protein 112

Basic information

Region (hg38): 17:65635536-66192133

Previous symbols: [ "CCDC46" ]

Links

ENSG00000154240 ∙ NCBI:201134 ∙ OMIM:618980 ∙ HGNC:28514 ∙ Uniprot:Q8N8E3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 44 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 44	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	31654588

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP112 gene.

• Inborn genetic diseases (41 variants)
• not provided (6 variants)
• not specified (1 variants)
• Spermatogenic failure 44 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP112 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				2	1	3
missense			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	42	4	1

Variants in CEP112

This is a list of pathogenic ClinVar variants found in the CEP112 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-65637177-C-A			Benign (Nov 14, 2018)
17-65637187-A-G		not specified	Uncertain significance (Dec 16, 2023)
17-65641007-A-G		not specified	Uncertain significance (Dec 15, 2022)
17-65641029-T-C		not specified	Uncertain significance (Dec 19, 2022)
17-65641056-T-C		not specified	Uncertain significance (Mar 07, 2024)
17-65689142-T-G		not specified	Uncertain significance (Jun 23, 2021)
17-65689153-G-T		not specified	Uncertain significance (Nov 09, 2023)
17-65689161-A-T		not specified	Uncertain significance (Jan 31, 2024)
17-65689170-C-G		not specified	Uncertain significance (Dec 16, 2023)
17-65689178-C-A		not specified	Uncertain significance (Apr 19, 2023)
17-65689206-C-T		not specified	Uncertain significance (Jul 26, 2021)
17-65743097-G-T		not specified	Uncertain significance (Dec 28, 2023)
17-65743123-T-C		not specified	Uncertain significance (Aug 30, 2022)
17-65750713-C-T			Likely benign (Mar 01, 2024)
17-65851809-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-65851868-G-A		not specified	Uncertain significance (Feb 10, 2023)
17-65851980-C-G		not specified	Uncertain significance (Dec 22, 2023)
17-65851980-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-65852022-T-C		not specified	Uncertain significance (Oct 25, 2022)
17-65852025-C-T		not specified	Uncertain significance (Mar 28, 2023)
17-65852037-T-A			Likely benign (Sep 01, 2023)
17-65902211-G-A		Spermatogenic failure 44	Pathogenic (Oct 12, 2020)
17-65902241-G-A		Spermatogenic failure 44 • not specified	Uncertain significance (May 04, 2022)
17-65902330-A-G		CEP112-related disorder	Likely benign (Feb 18, 2022)
17-65961487-T-G		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP112	protein_coding	protein_coding	ENST00000392769	26	556547

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.09e-39	0.0000295	125451	0	297	125748	0.00118

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0232	478	479	0.997	0.0000254	6318
Missense in Polyphen		159	178.48	0.89086		2426
Synonymous	0.151	166	168	0.985	0.00000868	1610
Loss of Function	0.668	62	67.9	0.912	0.00000377	791

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00157
Ashkenazi Jewish	0.000598	0.000595
East Asian	0.00170	0.00169
Finnish	0.00393	0.00393
European (Non-Finnish)	0.000764	0.000747
Middle Eastern	0.00170	0.00169
South Asian	0.00159	0.00157
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.69

Haploinsufficiency Scores

• pHI: 0.285
• hipred: N
• hipred_score: 0.368
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep112

Gene ontology

• Biological process: receptor localization to synapse
• Cellular component: cytoplasm;centrosome;plasma membrane;inhibitory synapse