C4orf17

chromosome 4 open reading frame 17

Basic information

Region (hg38): 4:99511012-99542303

Links

ENSG00000138813 ∙ NCBI:84103 ∙ ∙ HGNC:25274 ∙ Uniprot:Q53FE4 ∙ 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 C4orf17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C4orf17 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		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in C4orf17

This is a list of pathogenic ClinVar variants found in the C4orf17 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-99529854-G-T		not specified	Uncertain significance (Jul 27, 2021)
4-99529903-A-C		not specified	Likely benign (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C4orf17	protein_coding	protein_coding	ENST00000326581	8	31300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-8	0.196	125069	33	626	125728	0.00262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.603	162	185	0.875	0.00000851	2330
Missense in Polyphen		42	45.423	0.92464		624
Synonymous	0.431	62	66.5	0.933	0.00000327	698
Loss of Function	0.359	13	14.5	0.898	6.06e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0743	0.0373
Ashkenazi Jewish	0.000199	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000655	0.000396
Middle Eastern	0.00	0.00
South Asian	0.000167	0.000163
Other	0.00164	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0699

Intolerance Scores

• loftool: 0.859
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.65

Haploinsufficiency Scores

• pHI: 0.0764
• hipred: N
• hipred_score: 0.123
• ghis: 0.415

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: 4930579F01Rik