CCDC172

protein-coding

coiled-coil domain containing 172

Gene summary

Predicted to be located in sperm midpiece. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf96

MANE transcript

NM_198515.3

Inheritance

—

ClinVar variants

U:39B:3

Top phenotype

Meckel-Gruber syndrome

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr10:116,324,448-116,380,029

External References & Databases

Ensembl (ENSG00000182645)

Transcript & Mutation Effects

hg38 • Region Span ~55.6 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 CCDC172 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

Meckel-Gruber syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198515.3. 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			37 clinvar	3 clinvar		40
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	39	3	0	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198515.3	RefSeq	NP_940917.1	8	MANE Select
ENST00000333254.4	Ensembl	ENSP00000329860.3	8	MANE Select
ENST00000938958.1	Ensembl	ENSP00000609017.1	8	Standard
ENST00000938959.1	Ensembl	ENSP00000609018.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

cytoplasm
sperm midpiece

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333254
Coding exons: 8
Length: 55602
Individuals with no LoFs: 125714
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 125746
p: 0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0616	116	118	0.984	0.00000547	1748
Missense (PolyPhen)		16	23.478	0.68148		348
Synonymous	0.829	31	37.5	0.828	0.00000178	371
Loss of Function	1.33	9	14.4	0.623	6.48e-7	211

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000093	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00034	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.000068	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.05
RVIS percentile EVS: 49.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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