CCDC172

coiled-coil domain containing 172

Basic information

Region (hg38): 10:116324448-116380029

Previous symbols: [ "C10orf96" ]

Links

ENSG00000182645 ∙ NCBI:374355 ∙ ∙ HGNC:30524 ∙ Uniprot:P0C7W6 ∙ 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 CCDC172 gene.

• not_specified (35 variants)
• Meckel-Gruber_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC172 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198515.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			32	3		35
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC172	protein_coding	protein_coding	ENST00000333254	8	55602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000373	0.839	125714	0	32	125746	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0616	116	118	0.984	0.00000547	1748
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000348	0.000339
Ashkenazi Jewish	0.00	0.00
East Asian	0.000340	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000157	0.000149
Middle Eastern	0.000340	0.000326
South Asian	0.0000680	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.0679
• hipred: N
• hipred_score: 0.173
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc172

Gene ontology

• Cellular component: cytoplasm;sperm midpiece
• Molecular function: protein binding