CCDC47

coiled-coil domain containing 47

Basic information

Region (hg38): 17:63745255-63776351

Links

ENSG00000108588

∙ NCBI:57003 ∙ OMIM:618260 ∙ HGNC:24856 ∙ Uniprot:Q96A33 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

trichohepatoneurodevelopmental syndrome (Strong), mode of inheritance: AR
trichohepatoneurodevelopmental syndrome (Strong), mode of inheritance: AR
trichohepatoneurodevelopmental syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Trichohepatoneurodevelopmental syndrome	AR	Allergy/Immunology/Infectious	Among other findings, individuals have been described with susceptibility to infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Craniofacial; Dental; Dermatologic; Gastrointestinal; Musculoskeletal; Neurologic	30401460

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC47 gene.

not_specified (41 variants)
Trichohepatoneurodevelopmental_syndrome (8 variants)
not_provided (6 variants)
CCDC47-related_disorder (6 variants)
Global_developmental_delay_with_dysmorphic_features,_liver_dysfunction,_pruritus,_and_woolly_hair (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC47 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020198.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	1 clinvar	4
missense			42 clinvar			42
nonsense		3 clinvar				3
start loss						0
frameshift	1 clinvar	4 clinvar				5
splice donor/acceptor (+/-2bp)						0
Total	1	7	42	3	1

Highest pathogenic variant AF is 0.00000496354

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC47	protein_coding	protein_coding	ENST00000225726	12	31102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.13e-8	0.968	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	212	259	0.818	0.0000133	3249
Missense in Polyphen		66	85.422	0.77263		1023
Synonymous	0.158	85	86.9	0.979	0.00000418	831
Loss of Function	2.07	16	27.8	0.576	0.00000159	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.000362	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

loftool: 0.286
rvis_EVS: -0.62
rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

pHI: 0.466
hipred: N
hipred_score: 0.426
ghis: 0.620

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ccdc47
Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: osteoblast differentiation;ER overload response;endoplasmic reticulum organization;post-embryonic development;ubiquitin-dependent ERAD pathway;calcium ion homeostasis
Cellular component: endoplasmic reticulum;rough endoplasmic reticulum;membrane;integral component of membrane
Molecular function: RNA binding;calcium ion binding;protein binding