CCDC50

coiled-coil domain containing 50

Basic information

Region (hg38): 3:191329084-191398659

Previous symbols: [ "C3orf6", "DFNA44" ]

Links

ENSG00000152492 ∙ NCBI:152137 ∙ OMIM:611051 ∙ HGNC:18111 ∙ Uniprot:Q8IVM0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant nonsyndromic hearing loss 44 (Strong), mode of inheritance: AD
• autosomal dominant nonsyndromic hearing loss 44 (Limited), mode of inheritance: AD
• autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
• autosomal dominant nonsyndromic hearing loss 44 (Limited), mode of inheritance: Unknown
• nonsyndromic genetic hearing loss (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal dominant 44	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic	12483295; 17503326
Hearing loss has been reported to occur in the first decade (6-10 years)

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC50 gene.

• not provided (178 variants)
• not specified (39 variants)
• Inborn genetic diseases (19 variants)
• Autosomal dominant nonsyndromic hearing loss 44 (16 variants)
• CCDC50-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC50 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			2	18	4	24
missense			69	8	8	85
nonsense			2			2
start loss						0
frameshift	1		1			2
inframe indel				1		1
splice donor/acceptor (+/-2bp)			1			1
splice region			2	5	4	11
non coding			1	28	44	73
Total	1	0	76	55	56

Variants in CCDC50

This is a list of pathogenic ClinVar variants found in the CCDC50 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-191329088-A-G			Benign (Jan 13, 2019)
3-191329141-C-G			Benign (Dec 23, 2018)
3-191329218-G-A			Likely benign (May 20, 2019)
3-191329261-G-A			Likely benign (May 10, 2019)
3-191329292-G-A			Likely benign (Sep 02, 2019)
3-191329453-C-T			Likely benign (Dec 23, 2018)
3-191329612-C-G			Likely benign (Oct 20, 2018)
3-191329707-G-A			Conflicting classifications of pathogenicity (Apr 14, 2023)
3-191329719-G-A			Likely benign (Aug 21, 2018)
3-191329729-G-T			Uncertain significance (Dec 24, 2023)
3-191329743-A-G		not specified	Benign (Jan 31, 2024)
3-191329937-G-T			Benign (Nov 02, 2019)
3-191329942-T-G			Benign (Aug 20, 2019)
3-191329942-TG-T			Benign (Sep 13, 2019)
3-191329942-TGG-T			Benign (Sep 02, 2019)
3-191329942-TGGG-T			Benign (Aug 06, 2019)
3-191329946-G-C			Benign (Nov 02, 2019)
3-191329951-G-C			Benign (Aug 15, 2019)
3-191329954-G-A			Benign (Aug 20, 2019)
3-191329954-G-T			Benign (Sep 01, 2019)
3-191329971-A-G			Benign (Jan 25, 2019)
3-191329975-AGTAG-A			Benign (Nov 10, 2018)
3-191356994-AT-A			Benign (Aug 21, 2019)
3-191357007-T-TA			Benign (Aug 18, 2019)
3-191357084-C-G		not specified • Autosomal dominant nonsyndromic hearing loss 44	Benign (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC50	protein_coding	protein_coding	ENST00000392456	12	69594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.92e-7	0.998	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0720	258	261	0.987	0.0000142	3164
Missense in Polyphen		73	87.352	0.8357		1067
Synonymous	-0.174	95	92.9	1.02	0.00000493	847
Loss of Function	2.70	16	32.7	0.490	0.00000192	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in EGFR signaling. {ECO:0000269|PubMed:15314609}.
• Disease: DISEASE: Deafness, autosomal dominant, 44 (DFNA44) [MIM:607453]: A form of non-syndromic deafness characterized by initially moderate hearing loss that affects mainly low to mid frequencies. Later, it progresses to involve all the frequencies and leads to a profound hearing loss by the 6th decade. {ECO:0000269|PubMed:17503326}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.58

Haploinsufficiency Scores

• pHI: 0.0469
• hipred: Y
• hipred_score: 0.571
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.433

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc50

Gene ontology

• Biological process: sensory perception of sound
• Cellular component: cytosol
• Molecular function: protein binding;ubiquitin protein ligase binding