CCDC171

coiled-coil domain containing 171

Basic information

Region (hg38): 9:15553043-16061663

Previous symbols: [ "C9orf93" ]

Links

ENSG00000164989 ∙ NCBI:203238 ∙ ∙ HGNC:29828 ∙ Uniprot:Q6TFL3 ∙ 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 CCDC171 gene.

• not_specified (224 variants)
• not_provided (5 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC171 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173550.4. 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				1	1	2
missense			218	8	2	228
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	218	9	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC171	protein_coding	protein_coding	ENST00000380701	25	508767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.03e-47	2.43e-7	125240	1	507	125748	0.00202

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.32	900	660	1.36	0.0000340	8736
Missense in Polyphen		278	232.27	1.1969		3227
Synonymous	-4.13	321	240	1.34	0.0000120	2346
Loss of Function	0.146	72	73.3	0.982	0.00000400	930

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00576	0.00566
Ashkenazi Jewish	0.000511	0.000496
East Asian	0.00118	0.000870
Finnish	0.000789	0.000786
European (Non-Finnish)	0.00223	0.00217
Middle Eastern	0.00118	0.000870
South Asian	0.00344	0.00330
Other	0.00100	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.66

Haploinsufficiency Scores

• pHI: 0.180
• ghis: 0.390

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc171
• Phenotype: hematopoietic system phenotype; immune system phenotype