C3orf52

chromosome 3 open reading frame 52, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 3:112086335-112131004

Links

ENSG00000114529 ∙ NCBI:79669 ∙ OMIM:611956 ∙ HGNC:26255 ∙ Uniprot:Q5BVD1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypotrichosis 15 (Limited), mode of inheritance: AR
• hypotrichosis 15 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypotrichosis 15	AR	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	Dermatologic	32336749; 34309526

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C3orf52 gene.

• Hypotrichosis 15 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C3orf52 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			1	1		2
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			5			5
Total	1	0	7	1	0

Highest pathogenic variant AF is 0.00000657

Variants in C3orf52

This is a list of pathogenic ClinVar variants found in the C3orf52 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-112086441-G-T		Hypotrichosis 15	Pathogenic (Mar 29, 2024)
3-112102960-G-A		not specified	Likely benign (Aug 19, 2021)
3-112109580-GTTATT-G		Hypotrichosis 15	Pathogenic (Dec 21, 2022)
3-112109614-G-A			Uncertain significance (Jan 01, 2023)
3-112112988-T-A		Hypotrichosis 15	Pathogenic (Dec 21, 2022)
3-112113145-G-A			Uncertain significance (May 01, 2022)
3-112116658-CT-C			Uncertain significance (May 01, 2022)
3-112116742-T-C		not specified	Uncertain significance (Aug 16, 2021)
3-112116793-G-A		not specified	Uncertain significance (Oct 06, 2021)
3-112116834-A-G		not specified	Uncertain significance (Aug 16, 2021)
3-112116865-A-G		not specified	Uncertain significance (Oct 18, 2021)
3-112123498-C-T		not specified	Likely benign (Mar 15, 2024)
3-112123499-G-A		not specified	Uncertain significance (Apr 07, 2022)
3-112123514-A-G		not specified	Uncertain significance (Apr 24, 2024)
3-112123550-A-T		not specified	Uncertain significance (Feb 12, 2024)
3-112123556-C-T		not specified	Uncertain significance (Nov 09, 2024)
3-112123565-A-T		not specified	Uncertain significance (Apr 08, 2024)
3-112123586-T-C		not specified	Uncertain significance (Oct 30, 2023)
3-112123594-A-G		not specified	Uncertain significance (Nov 07, 2024)
3-112123645-C-G		not specified	Uncertain significance (Nov 22, 2021)
3-112123718-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-112123724-T-C		not specified	Uncertain significance (Oct 24, 2024)
3-112123754-A-C		not specified	Uncertain significance (Jun 28, 2023)
3-112125234-G-T		not specified	Uncertain significance (Dec 27, 2022)
3-112127027-T-A		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C3orf52	protein_coding	protein_coding	ENST00000431717	4	44670

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000862	0.342	124620	0	11	124631	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.855	97	124	0.784	0.00000582	1612
Missense in Polyphen		23	24.157	0.95212		361
Synonymous	1.41	38	50.8	0.749	0.00000261	492
Loss of Function	-0.0564	6	5.85	1.03	2.49e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000442
Middle Eastern	0.0000558	0.0000556
South Asian	0.0000703	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0631

Intolerance Scores

• loftool: 0.868
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.35

Haploinsufficiency Scores

• pHI: 0.0470
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: BC016579