C1orf105

chromosome 1 open reading frame 105

Basic information

Region (hg38): 1:172420684-172468831

Links

ENSG00000180999 ∙ NCBI:92346 ∙ ∙ HGNC:29591 ∙ Uniprot:O95561 ∙ 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 C1orf105 gene.

• not provided (32 variants)
• Glycosylphosphatidylinositol biosynthesis defect 16 (14 variants)
• Inborn genetic diseases (10 variants)
• Non-immune hydrops fetalis (1 variants)
• Global developmental delay (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf105 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
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	4	28	8	4	45
Total	1	4	29	8	4

Highest pathogenic variant AF is 0.00000657

Variants in C1orf105

This is a list of pathogenic ClinVar variants found in the C1orf105 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-172441758-T-G		not specified	Uncertain significance (Aug 30, 2022)
1-172441762-T-C			Likely benign (Feb 01, 2023)
1-172441764-C-A		Glycosylphosphatidylinositol biosynthesis defect 16	Pathogenic (Nov 29, 2022)
1-172441773-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-172441811-C-T		Glycosylphosphatidylinositol biosynthesis defect 16	Uncertain significance (Dec 28, 2022)
1-172441827-G-A		Glycosylphosphatidylinositol biosynthesis defect 16	Benign (Jan 31, 2024)
1-172441884-T-C		Glycosylphosphatidylinositol biosynthesis defect 16	Uncertain significance (Nov 15, 2018)
1-172441947-G-A			Benign/Likely benign (Mar 01, 2024)
1-172441964-A-G		Non-immune hydrops fetalis • Glycosylphosphatidylinositol biosynthesis defect 16	Conflicting classifications of pathogenicity (Mar 17, 2024)
1-172441979-A-G			Uncertain significance (Oct 01, 2022)
1-172441988-A-C		not specified	Uncertain significance (Feb 27, 2024)
1-172441988-A-G		Glycosylphosphatidylinositol biosynthesis defect 16	Likely pathogenic (Oct 15, 2018)
1-172442039-C-T			Uncertain significance (Aug 02, 2022)
1-172442049-G-A		Glycosylphosphatidylinositol biosynthesis defect 16	Uncertain significance (Jan 09, 2024)
1-172442057-A-C		Glycosylphosphatidylinositol biosynthesis defect 16	Likely pathogenic (Oct 15, 2018)
1-172442066-G-C		not specified	Uncertain significance (Sep 24, 2021)
1-172442090-G-A			Uncertain significance (Oct 04, 2022)
1-172442092-T-C			Likely benign (Apr 27, 2023)
1-172442093-A-G			Uncertain significance (Dec 07, 2023)
1-172442125-A-G			Benign (Dec 12, 2023)
1-172442178-T-C		not specified	Uncertain significance (Jun 13, 2022)
1-172442212-C-T			Likely benign (Oct 25, 2022)
1-172442230-A-G			Likely benign (Sep 19, 2023)
1-172442234-G-A		Glycosylphosphatidylinositol biosynthesis defect 16	Uncertain significance (Feb 27, 2022)
1-172442287-A-G			Likely benign (Jun 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf105	protein_coding	protein_coding	ENST00000367727	7	48144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000110	0.371	111498	599	13630	125727	0.0583

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.350	84	93.5	0.898	0.00000443	1199
Missense in Polyphen		8	6.002	1.3329		69
Synonymous	0.859	27	33.3	0.811	0.00000166	332
Loss of Function	0.295	8	8.95	0.894	3.77e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0667	0.0659
Ashkenazi Jewish	0.0965	0.0942
East Asian	0.00104	0.000489
Finnish	0.118	0.116
European (Non-Finnish)	0.0655	0.0638
Middle Eastern	0.00104	0.000489
South Asian	0.0684	0.0635
Other	0.0751	0.0729

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.784
• rvis_EVS: 0.73
• rvis_percentile_EVS: 85.98

Haploinsufficiency Scores

• pHI: 0.0532
• 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: 4930558K02Rik

Gene ontology

• Molecular function: protein binding