CCDC127

coiled-coil domain containing 127

Basic information

Region (hg38): 5:196868-218153

Links

ENSG00000164366 ∙ NCBI:133957 ∙ ∙ HGNC:30520 ∙ Uniprot:Q96BQ5 ∙ 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 CCDC127 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC127 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in CCDC127

This is a list of pathogenic ClinVar variants found in the CCDC127 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-205344-C-T		not specified	Uncertain significance (Feb 17, 2024)
5-205350-C-T		not specified	Likely benign (Jun 18, 2024)
5-205370-T-C		not specified	Uncertain significance (Jul 13, 2021)
5-205400-T-C		not specified	Uncertain significance (Jun 05, 2023)
5-205433-T-C		not specified	Uncertain significance (Jun 29, 2022)
5-205474-G-C		not specified	Uncertain significance (Jun 18, 2024)
5-205494-C-T		not specified	Uncertain significance (Jun 23, 2021)
5-205500-C-A		not specified	Uncertain significance (Jul 14, 2023)
5-205506-C-A		not specified	Uncertain significance (Jul 20, 2022)
5-205533-G-A		not specified	Uncertain significance (Nov 06, 2023)
5-205542-G-A		not specified	Uncertain significance (Aug 12, 2021)
5-205559-C-T		not specified	Uncertain significance (Mar 03, 2022)
5-205580-G-A		not specified	Uncertain significance (Dec 27, 2022)
5-205686-T-C		not specified	Uncertain significance (Dec 21, 2023)
5-205728-T-C		not specified	Uncertain significance (Mar 06, 2023)
5-205760-A-G		not specified	Uncertain significance (Mar 05, 2024)
5-205766-G-A		not specified	Uncertain significance (Mar 20, 2024)
5-205769-T-A		not specified	Uncertain significance (Jul 09, 2021)
5-205820-T-C		not specified	Uncertain significance (Jul 19, 2023)
5-205847-A-G		not specified	Uncertain significance (Nov 03, 2022)
5-205898-C-T		not specified	Likely benign (Jun 01, 2023)
5-205907-G-T		not specified	Uncertain significance (Jan 03, 2022)
5-205916-T-G		not specified	Uncertain significance (Jul 19, 2022)
5-216750-T-C		not specified	Uncertain significance (Jun 06, 2023)
5-216797-G-A		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC127	protein_coding	protein_coding	ENST00000296824	2	21345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000473	0.883	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.611	131	152	0.861	0.00000927	1693
Missense in Polyphen		46	58.697	0.78368		658
Synonymous	-1.43	73	59.1	1.24	0.00000358	496
Loss of Function	1.40	7	12.3	0.570	7.92e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000229	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000443	0.000440
Middle Eastern	0.000229	0.000217
South Asian	0.000167	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.420
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.346
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.447

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc127
• Phenotype: immune system phenotype; hematopoietic system phenotype