CLMN

calmin

Basic information

Region (hg38): 14:95181939-95319908

Links

ENSG00000165959 ∙ NCBI:79789 ∙ OMIM:611121 ∙ HGNC:19972 ∙ Uniprot:Q96JQ2 ∙ 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 CLMN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLMN 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				9	7	16
missense			67	8	5	80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	2	5
non coding					1	1
Total	0	0	67	17	13

Variants in CLMN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-95191581-C-T		not specified	Uncertain significance (May 11, 2022)
14-95191630-A-C		not specified	Uncertain significance (Mar 19, 2024)
14-95191632-T-A		not specified	Uncertain significance (May 31, 2023)
14-95191653-G-T		not specified	Uncertain significance (Aug 17, 2021)
14-95191685-G-A			Benign (Dec 31, 2019)
14-95191691-T-C		not specified	Uncertain significance (Oct 12, 2022)
14-95191724-T-C		not specified	Uncertain significance (Oct 21, 2021)
14-95193845-C-T		CLMN-related disorder	Benign (Jul 10, 2019)
14-95193905-A-G		CLMN-related disorder	Benign (Oct 21, 2019)
14-95193906-T-C		CLMN-related disorder	Likely benign (Dec 15, 2022)
14-95194543-G-A		not specified	Likely benign (Mar 02, 2023)
14-95196508-T-A		CLMN-related disorder	Benign (Dec 31, 2019)
14-95196517-C-T		not specified	Uncertain significance (Oct 05, 2023)
14-95196552-A-G		not specified	Uncertain significance (May 04, 2023)
14-95196654-A-G		not specified	Uncertain significance (Feb 26, 2024)
14-95196656-G-A		CLMN-related disorder	Likely benign (Jul 30, 2019)
14-95196666-A-C		not specified	Uncertain significance (Nov 18, 2023)
14-95202828-G-A			Benign (Dec 31, 2019)
14-95202850-C-T		not specified	Uncertain significance (Jun 02, 2023)
14-95202894-G-A		not specified	Uncertain significance (Jul 20, 2021)
14-95202924-G-A		not specified	Uncertain significance (Jul 15, 2021)
14-95202926-G-A		not specified	Uncertain significance (Aug 21, 2023)
14-95202963-G-T		not specified	Uncertain significance (Mar 27, 2023)
14-95202997-C-T			Benign (Nov 27, 2018)
14-95203037-T-G			Likely benign (Nov 27, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLMN	protein_coding	protein_coding	ENST00000298912	13	137967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-8	1.00	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.184	540	552	0.978	0.0000293	6645
Missense in Polyphen		145	156.88	0.92428		1981
Synonymous	-0.149	228	225	1.01	0.0000138	1903
Loss of Function	3.11	20	41.6	0.480	0.00000232	491

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000539	0.000528
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00109	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.000393	0.000387
Middle Eastern	0.00109	0.00109
South Asian	0.000363	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Vitamin D Receptor Pathway (Consensus)

Recessive Scores

• pRec: 0.0872

Intolerance Scores

• loftool: 0.100
• rvis_EVS: -0.74
• rvis_percentile_EVS: 13.78

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.270
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.451

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clmn

Gene ontology

• Biological process: nuclear migration;negative regulation of cell population proliferation;neuron projection development;nucleus localization;cytoskeletal anchoring at nuclear membrane
• Cellular component: nuclear outer membrane;cytoplasm;integral component of membrane;meiotic nuclear membrane microtubule tethering complex
• Molecular function: actin filament binding