CCDC154

coiled-coil domain containing 154

Basic information

Region (hg38): 16:1434383-1444556

Previous symbols: [ "C16orf29" ]

Links

ENSG00000197599 ∙ NCBI:645811 ∙ OMIM:618740 ∙ HGNC:34454 ∙ Uniprot:A6NI56 ∙ 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 CCDC154 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC154 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			73	20		93
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding			3	1		4
Total	0	0	76	22	0

Variants in CCDC154

This is a list of pathogenic ClinVar variants found in the CCDC154 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1434452-C-G		not specified	Uncertain significance (Sep 29, 2023)
16-1434476-C-T		not specified	Uncertain significance (Dec 28, 2022)
16-1434482-C-G		not specified	Likely benign (Jan 21, 2025)
16-1434490-C-T		not specified	Likely benign (Mar 01, 2023)
16-1434514-G-C		not specified	Uncertain significance (Jan 26, 2023)
16-1434526-C-T		not specified	Uncertain significance (Jan 22, 2024)
16-1434535-C-T			Likely benign (Mar 01, 2023)
16-1434674-G-A		not specified	Uncertain significance (Apr 27, 2024)
16-1434675-C-A		not specified	Uncertain significance (Mar 15, 2024)
16-1434719-G-A		not specified	Uncertain significance (Nov 21, 2022)
16-1434735-A-C		not specified	Uncertain significance (Oct 03, 2022)
16-1434740-C-T		not specified	Likely benign (Sep 26, 2023)
16-1434741-G-A		not specified	Uncertain significance (Mar 18, 2024)
16-1434743-G-A		not specified	Likely benign (Sep 30, 2021)
16-1434789-G-A		not specified	Likely benign (Apr 28, 2022)
16-1434813-G-A		not specified	Uncertain significance (Nov 25, 2024)
16-1434852-G-A		not specified	Uncertain significance (Apr 22, 2022)
16-1435115-G-A		not specified	Uncertain significance (Aug 30, 2021)
16-1435137-C-A		not specified	Uncertain significance (Oct 16, 2023)
16-1435142-C-T		not specified	Likely benign (May 23, 2023)
16-1435155-C-A		not specified	Uncertain significance (Jul 10, 2024)
16-1435986-G-C		not specified	Uncertain significance (Mar 01, 2025)
16-1436004-G-A		not specified	Uncertain significance (Oct 04, 2024)
16-1436034-C-T		not specified	Uncertain significance (Dec 19, 2022)
16-1436458-C-T		not specified	Uncertain significance (Nov 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC154	protein_coding	protein_coding	ENST00000389176	17	10174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.25e-17	0.0559	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.518	359	388	0.926	0.0000262	4239
Missense in Polyphen		82	102.98	0.79625		1367
Synonymous	-0.196	191	188	1.02	0.0000130	1402
Loss of Function	0.859	28	33.4	0.839	0.00000151	406

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.187

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc154

Gene ontology

• Cellular component: early endosome