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
• hypotrichosis 15 (Moderate), 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 (4 variants)
• not_provided (2 variants)
• not_specified (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. These statistics are base on transcript: NM_000024616.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			1	1		2
nonsense	3					3
start loss						0
frameshift	1					1
splice donor/acceptor (+/-2bp)			1			1
Total	4	0	2	1	0

Highest pathogenic variant AF is 0.000009671043

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