C1orf167

chromosome 1 open reading frame 167

Basic information

Region (hg38): 1:11761786-11789585

Links

ENSG00000215910 ∙ NCBI:284498 ∙ ∙ HGNC:25262 ∙ Uniprot:Q5SNV9 ∙ 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 C1orf167 gene.

• Neural tube defects, folate-sensitive (9 variants)
• Homocystinuria due to methylene tetrahydrofolate reductase deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf167 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			1			1
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1	1	7
Total	0	0	8	1	1

Variants in C1orf167

This is a list of pathogenic ClinVar variants found in the C1orf167 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-11786035-G-GT		Neural tube defects, folate-sensitive	Benign (Jun 14, 2016)
1-11786191-A-G		Neural tube defects, folate-sensitive	Uncertain significance (Jun 14, 2016)
1-11786602-ATTTT-A		Neural tube defects, folate-sensitive	Likely benign (Jun 14, 2016)
1-11786602-ATTTTTTTT-A		Neural tube defects, folate-sensitive	Uncertain significance (Jun 14, 2016)
1-11786602-A-ATT		Neural tube defects, folate-sensitive	Uncertain significance (Jun 14, 2016)
1-11786618-TTTTG-T		Neural tube defects, folate-sensitive	Uncertain significance (Jun 14, 2016)
1-11788023-G-A		Homocystinuria due to methylene tetrahydrofolate reductase deficiency	Conflicting classifications of pathogenicity (Feb 01, 2024)
1-11788203-CCTT-C		Neural tube defects, folate-sensitive	Uncertain significance (Jun 14, 2016)
1-11788224-C-T		Neural tube defects, folate-sensitive	Uncertain significance (Jun 14, 2016)
1-11789149-G-A		Neural tube defects, folate-sensitive	Uncertain significance (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf167	protein_coding	protein_coding	ENST00000433342	21	27799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.15e-34	0.00114	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	645	730	0.884	0.0000427	9169
Missense in Polyphen		15	17.021	0.88125		180
Synonymous	2.60	247	305	0.810	0.0000170	3107
Loss of Function	1.19	57	67.6	0.843	0.00000366	711

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: 0.0769
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N

Gene Damage Prediction

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