CNEP1R1

CTD nuclear envelope phosphatase 1 regulatory subunit 1

Basic information

Region (hg38): 16:50024410-50037088

Previous symbols: [ "C16orf69", "TMEM188" ]

Links

ENSG00000205423 ∙ NCBI:255919 ∙ OMIM:616869 ∙ HGNC:26759 ∙ Uniprot:Q8N9A8 ∙ 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 CNEP1R1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNEP1R1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in CNEP1R1

This is a list of pathogenic ClinVar variants found in the CNEP1R1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-50026404-G-A		not specified	Uncertain significance (Mar 21, 2024)
16-50026414-G-A		not specified	Uncertain significance (Jan 02, 2025)
16-50026418-A-T		not specified	Uncertain significance (Feb 07, 2025)
16-50029743-C-G		not specified	Uncertain significance (Jul 30, 2024)
16-50034119-G-A		not specified	Uncertain significance (Oct 21, 2024)
16-50034140-A-G		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNEP1R1	protein_coding	protein_coding	ENST00000458059	7	12679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.409	0.584	124633	0	2	124635	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	26	69.5	0.374	0.00000316	902
Missense in Polyphen		7	19.908	0.35161		289
Synonymous	-0.000620	24	24.0	1.00	0.00000113	276
Loss of Function	2.24	2	9.42	0.212	3.98e-7	121

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)	0.0000182	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms with the serine/threonine protein phosphatase CTDNEP1 an active complex which dephosphorylates and may activate LPIN1 and LPIN2. LPIN1 and LPIN2 are phosphatidate phosphatases that catalyze the conversion of phosphatidic acid to diacylglycerol and control the metabolism of fatty acids at different levels. May indirectly modulate the lipid composition of nuclear and/or endoplasmic reticulum membranes and be required for proper nuclear membrane morphology and/or dynamics. May also indirectly regulate the production of lipid droplets and triacylglycerol. {ECO:0000269|PubMed:22134922}.
• Pathway: Depolymerisation of the Nuclear Lamina;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Intolerance Scores

• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.37

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.528

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	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cnep1r1

Gene ontology

• Biological process: lipid metabolic process;mitotic nuclear envelope disassembly;positive regulation of triglyceride biosynthetic process;protein localization to nucleus;positive regulation of protein dephosphorylation
• Cellular component: nuclear envelope;cytoplasm;cytosol;integral component of membrane;nuclear membrane;Nem1-Spo7 phosphatase complex
• Molecular function: protein binding