C1orf127

chromosome 1 open reading frame 127

Basic information

Region (hg38): 1:10946471-10982076

Links

ENSG00000175262 ∙ NCBI:148345 ∙ OMIM:619700 ∙ HGNC:26730 ∙ Uniprot:Q8N9H9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Heterotaxy, visceral, 14, autosomal	AR	Cardiovascular	The condition may involve congenital cardiac and other anomalies, and awareness may allow early diagnosis and interventions	Cardiovascular; Gastrointestinal; Renal	39753129

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C1orf127 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf127 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			6	1	1	8
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	1

Variants in C1orf127

This is a list of pathogenic ClinVar variants found in the C1orf127 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-10947824-G-T		not specified	Uncertain significance (Jul 09, 2021)
1-10947886-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-10948070-C-T			Benign (Aug 08, 2017)
1-10948249-C-A		not specified	Uncertain significance (Aug 09, 2021)
1-10948703-G-A		not specified	Uncertain significance (Oct 05, 2021)
1-10949661-C-T		not specified	Likely benign (Jul 08, 2021)
1-10949703-TG-T		HETEROTAXY, VISCERAL, 14, AUTOSOMAL	Pathogenic (Jan 31, 2025)
1-10955178-G-T		not specified	Uncertain significance (Aug 09, 2021)
1-10957106-A-G		not specified	Uncertain significance (Jun 11, 2021)
1-10957732-G-A		HETEROTAXY, VISCERAL, 14, AUTOSOMAL	Pathogenic (Jan 31, 2025)
1-10966393-G-A		not specified	Uncertain significance (Sep 02, 2024)
1-10976227-G-A		HETEROTAXY, VISCERAL, 14, AUTOSOMAL	Pathogenic (Jan 31, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf127	protein_coding	protein_coding	ENST00000377004	12	35567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.49e-11	0.561	125718	0	11	125729	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.660	423	463	0.914	0.0000260	5139
Missense in Polyphen		115	133.81	0.85943		1572
Synonymous	0.394	193	200	0.965	0.0000123	1842
Loss of Function	1.38	21	29.0	0.723	0.00000160	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000528
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.822
• rvis_EVS: 0.99
• rvis_percentile_EVS: 90.48

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.179
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Gm572
• Phenotype: cellular phenotype; growth/size/body region phenotype; immune system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype

Gene ontology

• Biological process: heart development