CCDC51

coiled-coil domain containing 51

Basic information

Region (hg38): 3:48432164-48440456

Links

ENSG00000164051 ∙ NCBI:79714 ∙ OMIM:618585 ∙ HGNC:25714 ∙ Uniprot:Q96ER9 ∙ 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 CCDC51 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC51 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					1	1
missense			21	1	2	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	21	1	3

Variants in CCDC51

This is a list of pathogenic ClinVar variants found in the CCDC51 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48432591-T-A		not specified	Uncertain significance (Nov 15, 2024)
3-48432613-G-C		not specified	Uncertain significance (May 24, 2024)
3-48432637-C-T		not specified • Retinal dystrophy	Uncertain significance (Dec 14, 2023)
3-48432676-T-C			Benign (Dec 28, 2017)
3-48432711-C-A		not specified	Uncertain significance (Jun 29, 2023)
3-48432749-G-A		not specified	Uncertain significance (Mar 03, 2022)
3-48432770-T-C		not specified	Uncertain significance (Sep 23, 2023)
3-48432775-G-A		not specified	Uncertain significance (Apr 13, 2022)
3-48432782-T-G		not specified	Uncertain significance (Aug 14, 2024)
3-48432853-T-C		not specified	Uncertain significance (Apr 17, 2024)
3-48432875-G-A		not specified	Uncertain significance (Dec 06, 2022)
3-48432889-G-A		not specified	Uncertain significance (Aug 20, 2024)
3-48432967-C-G		not specified	Uncertain significance (Oct 21, 2024)
3-48432973-C-T		not specified	Uncertain significance (Mar 31, 2024)
3-48432982-T-G		not specified	Uncertain significance (Nov 26, 2024)
3-48433064-G-A		not specified	Uncertain significance (Jan 04, 2024)
3-48433085-G-A		not specified	Uncertain significance (Oct 13, 2023)
3-48433151-G-A			Benign (Dec 28, 2017)
3-48433165-T-C		not specified	Uncertain significance (Oct 24, 2023)
3-48433735-A-T		not specified	Uncertain significance (Aug 05, 2024)
3-48433736-G-T		not specified	Uncertain significance (Aug 05, 2024)
3-48433768-C-T		not specified	Uncertain significance (Jan 17, 2024)
3-48433778-G-A		not specified	Uncertain significance (Mar 01, 2024)
3-48433792-T-C		not specified	Uncertain significance (Dec 12, 2023)
3-48433844-C-G		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC51	protein_coding	protein_coding	ENST00000395694	3	8293

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.11e-8	0.529	124713	0	85	124798	0.000341

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	190	237	0.803	0.0000134	2634
Missense in Polyphen		49	65.799	0.74469		765
Synonymous	0.934	82	93.5	0.877	0.00000489	887
Loss of Function	1.02	14	18.8	0.746	0.00000144	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000705	0.000702
Ashkenazi Jewish	0.00	0.00
East Asian	0.000723	0.000723
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000233	0.000230
Middle Eastern	0.000723	0.000723
South Asian	0.000490	0.000490
Other	0.000827	0.000825

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.0989
• hipred: N
• hipred_score: 0.204
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc51

Gene ontology

• Cellular component: integral component of membrane