C3orf49

chromosome 3 open reading frame 49

Basic information

Region (hg38): 3:63819298-63848636

Links

ENSG00000163632 ∙ NCBI:132200 ∙ ∙ HGNC:25190 ∙ Uniprot:Q96BT1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C3orf49 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C3orf49 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11			11
Total	0	0	11	0	0

Variants in C3orf49

This is a list of pathogenic ClinVar variants found in the C3orf49 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-63834169-G-A		not specified	Uncertain significance (Oct 29, 2021)
3-63834172-T-G		not specified	Uncertain significance (Dec 28, 2022)
3-63835345-A-C		not specified	Uncertain significance (Feb 22, 2023)
3-63835387-T-G		not specified	Uncertain significance (Jun 09, 2022)
3-63836325-T-G		not specified	Uncertain significance (Apr 08, 2022)
3-63838045-C-T		not specified	Uncertain significance (Nov 22, 2022)
3-63838387-T-C		not specified	Uncertain significance (Dec 12, 2023)
3-63838440-T-C		not specified	Uncertain significance (Dec 19, 2022)
3-63838447-T-C		not specified	Uncertain significance (Oct 04, 2022)
3-63838470-G-A		not specified	Uncertain significance (Mar 22, 2023)
3-63838478-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-63838490-C-A		not specified	Uncertain significance (Apr 07, 2022)
3-63838491-T-G		not specified	Uncertain significance (Apr 07, 2022)
3-63839690-T-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C3orf49	protein_coding	protein_coding	ENST00000295896	6	29275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.06e-8	0.207	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	102	139	0.735	0.00000664	1895
Missense in Polyphen		22	33.152	0.66361		490
Synonymous	2.19	31	50.9	0.609	0.00000234	548
Loss of Function	0.299	12	13.2	0.911	6.13e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.111
• ghis: 0.383

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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