CLMN

calmin

Basic information

Region (hg38): 14:95181940-95319908

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.

• not_specified (148 variants)
• not_provided (20 variants)
• CLMN-related_disorder (18 variants)

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. These statistics are base on transcript: NM_000024734.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				11	5	16
missense			137	15	5	157
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	137	26	10

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