CCDC141

coiled-coil domain containing 141, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 2:178829757-179050137

Links

ENSG00000163492 ∙ NCBI:285025 ∙ OMIM:616031 ∙ HGNC:26821 ∙ Uniprot:Q6ZP82 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Kallmann syndrome (Supportive), mode of inheritance: AD
• hypogonadotropic hypogonadism (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC141 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC141 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			1	39	6	46
missense			141	24	11	176
nonsense			4	1		5
start loss						0
frameshift			5			5
inframe indel			2			2
splice donor/acceptor (+/-2bp)			1			1
splice region			5	4	1	10
non coding				5	65	70
Total	0	0	154	69	82

Variants in CCDC141

This is a list of pathogenic ClinVar variants found in the CCDC141 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-178833869-G-A			Benign (Nov 10, 2018)
2-178834117-G-A			Benign (Nov 10, 2018)
2-178834180-G-C		not specified	Uncertain significance (Dec 02, 2021)
2-178834218-G-A			Benign (Jan 26, 2024)
2-178834227-G-A			Likely benign (Apr 16, 2018)
2-178834267-C-A		not specified	Uncertain significance (Jan 23, 2024)
2-178834269-T-C			Uncertain significance (Oct 17, 2022)
2-178834270-G-C			Uncertain significance (Aug 02, 2021)
2-178834280-G-A			Uncertain significance (Dec 20, 2022)
2-178834304-C-T			Benign (Dec 19, 2022)
2-178834306-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-178834322-G-A		not specified	Uncertain significance (Oct 03, 2022)
2-178834329-A-C			Uncertain significance (Nov 24, 2023)
2-178834340-C-T			Uncertain significance (Aug 17, 2023)
2-178834349-T-C		not specified	Likely benign (May 30, 2024)
2-178834355-C-T		not specified	Uncertain significance (May 15, 2023)
2-178834377-C-A		not specified	Uncertain significance (Nov 07, 2023)
2-178834382-T-A		not specified	Uncertain significance (Jan 24, 2024)
2-178834383-C-T			Likely benign (Feb 10, 2023)
2-178834397-C-T		Hypogonadotropic hypogonadism 7 with or without anosmia	Likely benign (Mar 01, 2024)
2-178834415-C-G		not specified	Uncertain significance (Oct 12, 2022)
2-178834419-C-A		not specified • CCDC141-related disorder	Uncertain significance (Jan 30, 2024)
2-178834657-A-G			Benign (Jun 18, 2021)
2-178836907-G-A		Hypogonadotropic hypogonadism	Uncertain significance (May 29, 2020)
2-178836924-A-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC141	protein_coding	protein_coding	ENST00000420890	24	220330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.59e-33	0.00587	125585	0	156	125741	0.000621

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0354	750	747	1.00	0.0000377	10093
Missense in Polyphen		207	214.11	0.9668		3291
Synonymous	0.516	271	282	0.961	0.0000150	2777
Loss of Function	1.57	59	73.5	0.803	0.00000351	976

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000924	0.000784
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000942	0.000925
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000383	0.000360
Middle Eastern	0.000942	0.000925
South Asian	0.00245	0.00242
Other	0.000356	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a critical role in radial migration and centrosomal function. {ECO:0000250|UniProtKB:A2AST1}.

Recessive Scores

• pRec: 0.0869

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.206
• ghis: 0.451

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.557

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc141
• Phenotype: cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: cytoplasm;microtubule organizing center
• Molecular function: protein binding