CNTLN

centlein

Basic information

Region (hg38): 9:17134982-17503923

Previous symbols: [ "C9orf101", "C9orf39" ]

Links

ENSG00000044459 ∙ NCBI:54875 ∙ OMIM:611870 ∙ HGNC:23432 ∙ Uniprot:Q9NXG0 ∙ 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 CNTLN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTLN 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					3	3
missense			99	4	3	106
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	99	4	7

Variants in CNTLN

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

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

Position	Type	Phenotype	Significance	ClinVar
9-17135105-C-T		not specified	Uncertain significance (Mar 17, 2023)
9-17135124-C-A		not specified	Uncertain significance (Feb 09, 2023)
9-17135151-C-T		not specified	Uncertain significance (Jan 16, 2024)
9-17135175-A-T		not specified	Uncertain significance (Jun 18, 2024)
9-17135181-C-T		not specified	Uncertain significance (Feb 05, 2024)
9-17135233-C-G		not specified	Uncertain significance (Jan 19, 2024)
9-17135246-G-A		not specified	Uncertain significance (Feb 02, 2024)
9-17135274-G-C		not specified	Uncertain significance (Nov 08, 2022)
9-17135276-G-A		not specified	Likely benign (Sep 20, 2023)
9-17135279-G-A		not specified	Uncertain significance (Dec 06, 2023)
9-17135280-C-T		not specified	Uncertain significance (Aug 16, 2022)
9-17135289-C-G		not specified	Uncertain significance (Jan 24, 2024)
9-17135300-C-G		not specified	Uncertain significance (Feb 10, 2022)
9-17135307-G-T		not specified	Uncertain significance (Mar 02, 2023)
9-17135317-G-T		not specified	Uncertain significance (Feb 14, 2024)
9-17143292-A-T		not specified	Uncertain significance (May 24, 2023)
9-17143296-A-C		not specified	Uncertain significance (Dec 12, 2023)
9-17143310-C-G		not specified	Uncertain significance (Oct 14, 2023)
9-17143354-G-A		not specified	Uncertain significance (May 11, 2022)
9-17235661-G-C		not specified	Uncertain significance (Jun 10, 2024)
9-17235668-T-C		not specified	Uncertain significance (Jan 03, 2024)
9-17235691-C-T		not specified	Uncertain significance (Jun 29, 2022)
9-17235700-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-17235772-G-C		not specified	Uncertain significance (Jul 15, 2021)
9-17236562-A-C		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTLN	protein_coding	protein_coding	ENST00000380647	26	368942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.95e-49	1.35e-7	123853	6	942	124801	0.00381

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.37	844	671	1.26	0.0000324	9224
Missense in Polyphen		242	192.85	1.2549		2925
Synonymous	-3.56	309	239	1.29	0.0000111	2451
Loss of Function	0.164	75	76.6	0.980	0.00000393	1005

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00307	0.00303
Ashkenazi Jewish	0.00141	0.00139
East Asian	0.000420	0.000389
Finnish	0.00855	0.00843
European (Non-Finnish)	0.00574	0.00526
Middle Eastern	0.000420	0.000389
South Asian	0.00166	0.00150
Other	0.00494	0.00463

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for centrosome cohesion and recruitment of CEP68 to centrosomes. {ECO:0000269|PubMed:24554434}.

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.983
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.29

Haploinsufficiency Scores

• pHI: 0.206
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.770

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntln

Gene ontology

• Biological process: centriole-centriole cohesion;protein localization to organelle
• Cellular component: nucleoplasm;cytoplasm;centrosome;centriole;cytosol;extracellular exosome
• Molecular function: protein kinase binding;protein domain specific binding;protein binding, bridging