CCDC154

protein-coding

coiled-coil domain containing 154

Gene summary

Predicted to be involved in bone mineralization involved in bone maturation. Predicted to act upstream of or within bone resorption; odontogenesis of dentin-containing tooth; and sensory perception of sound. Predicted to be located in early endosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C16orf29

MANE transcript

NM_001143980.3

Inheritance

—

ClinVar variants

U:123B:29

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr16:1,434,383-1,444,556

External References & Databases

Ensembl (ENSG00000197599)

Transcript & Mutation Effects

hg38 • Region Span ~10.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC154 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 151

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001143980.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			123 clinvar	28 clinvar		151
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1 clinvar		1
Total	0	0	123	29	0	152

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001143980.3	RefSeq	NP_001137452.1	17	MANE Select
ENST00000389176.4	Ensembl	ENSP00000373828.4	17	MANE Select
ENST00000409671.5	Ensembl	ENSP00000386744.1	14	Standard
ENST00000409671.6	Ensembl	ENSP00000386744.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

early endosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389176
Coding exons: 17
Length: 10174
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.518	359	388	0.926	0.0000262	4239
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.187

Gene Damage Prediction

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