C1orf105

Gene

chromosome 1 open reading frame 105

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

MANE transcript

NM_139240.4

Inheritance

—

ClinVar variants

U:3

Top phenotype

Glycosylphosphatidylinositol biosynthesis defect 16

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr1:172,420,685-172,468,831

External References & Databases

Ensembl (ENSG00000180999)

Transcript & Mutation Effects

hg38 • Region Span ~48.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1orf105 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 43

Glycosylphosphatidylinositol biosynthesis defect 16Total: 20

Non-immune hydrops fetalisTotal: 1

Global developmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139240.4. 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						0
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	3	0	0	3

Highest pathogenic variant AF is 0.000072492505

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139240.4	RefSeq	NP_640333.3	7	MANE Select
ENST00000367727.9	Ensembl	ENSP00000356700.4	7	MANE Select
NM_001300760.1	RefSeq	NP_001287689.1	5	Standard
ENST00000367725.4	Ensembl	ENSP00000356698.4	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367727
Coding exons: 7
Length: 48144
Individuals with no LoFs: 111498
Homozygous LoFs: 599
Heterozygous LoFs: 13630
Defined: 125727
p: 0.0583

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.350	84	93.5	0.898	0.00000443	1199
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.032	0.031	notable
Latino/Admixed American	0.035	0.033	notable
Ashkenazi Jewish	0.097	0.094	notable
East Asian	0.0010	0.00049	notable
Finnish	0.12	0.12	notable
European (Non-Finnish)	0.066	0.064	notable
South Asian	0.068	0.064	notable
Other	0.075	0.073	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.784
RVIS EVS: 0.73
RVIS percentile EVS: 85.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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