CCDC47

protein-coding

coiled-coil domain containing 47

Gene summary

Enables protein folding chaperone and ribosome binding activity. Involved in ERAD pathway; endoplasmic reticulum calcium ion homeostasis; and multi-pass transmembrane protein insertion into ER membrane. Located in endoplasmic reticulum membrane. Part of multi-pass translocon complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020198.3

Inheritance

ClinVar variants

P:8U:56B:5

Top phenotype

Trichohepatoneurodevelopmental syndrome

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr17:63,745,255-63,776,351

External References & Databases

Ensembl (ENSG00000108588)

Transcript & Mutation Effects

hg38 • Region Span ~31.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

trichohepatoneurodevelopmental syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032645

Submitter: G2P

trichohepatoneurodevelopmental syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032645

Submitter: Labcorp Genetics (formerly Invitae)

trichohepatoneurodevelopmental syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0032645

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Trichohepatoneurodevelopmental syndromeAR

Manifestation: Allergy/Immunology/Infectious; Craniofacial; Dental; Dermatologic; Gastrointestinal; Musculoskeletal; Neurologic

Intervention: Allergy/Immunology/Infectious

Rationale: Among other findings, individuals have been described with susceptibility to infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial

Refs: 30401460

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC47 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 50

Trichohepatoneurodevelopmental syndromeTotal: 9

not providedTotal: 8

CCDC47-related disorderTotal: 6

Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hairTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020198.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar	1 clinvar	5
missense			53 clinvar	1 clinvar		54
nonsense		3 clinvar				3
start loss						0
frameshift	1 clinvar	4 clinvar				5
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	7	56	4	1	69

Highest pathogenic variant AF is 0.0000049635364

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020198.3	RefSeq	NP_064583.2	12	MANE Select
ENST00000225726.10	Ensembl	ENSP00000225726.5	12	MANE Select
ENST00000403162.7	Ensembl	ENSP00000384888.3	12	Standard
ENST00000403162.8	Ensembl	ENSP00000384888.3	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

osteoblast differentiation
ER overload response
endoplasmic reticulum organization
post-embryonic development
ubiquitin-dependent ERAD pathway

Molecular Function

RNA binding
calcium ion binding
protein binding

Cellular Component

endoplasmic reticulum
rough endoplasmic reticulum
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000225726
Coding exons: 12
Length: 31102
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	212	259	0.818	0.0000133	3249
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00036	0.00036	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.286
RVIS EVS: -0.62
RVIS percentile EVS: 17.16

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.910

Gene Damage Prediction

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