C4orf54

chromosome 4 open reading frame 54

Basic information

Region (hg38): 4:99636529-99657828

Links

ENSG00000248713 ∙ NCBI:285556 ∙ OMIM:617881 ∙ HGNC:27741 ∙ Uniprot:D6RIA3 ∙ 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 C4orf54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C4orf54 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	9	1	11
missense				5	3	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	1	15	4

Variants in C4orf54

This is a list of pathogenic ClinVar variants found in the C4orf54 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-99649496-G-A			Likely benign (Jun 01, 2023)
4-99649820-C-T			Benign (Feb 01, 2023)
4-99649939-C-T			Likely benign (May 01, 2022)
4-99650405-A-G			Likely benign (Aug 01, 2022)
4-99650444-G-T			Likely benign (Dec 01, 2022)
4-99650746-C-T			Likely benign (May 01, 2022)
4-99651552-G-A			Likely benign (Oct 01, 2024)
4-99651793-G-C			Likely benign (May 01, 2022)
4-99652026-C-G			Benign (Feb 01, 2023)
4-99652174-G-A			Likely benign (Jun 01, 2022)
4-99652385-T-C			Likely benign (Oct 01, 2024)
4-99652687-G-T			Likely benign (Mar 01, 2022)
4-99652808-C-A			Likely benign (Mar 01, 2023)
4-99653131-G-A			Likely benign (May 01, 2022)
4-99653155-C-T			Likely benign (Apr 01, 2022)
4-99653719-A-T			Uncertain significance (Jan 01, 2024)
4-99653733-C-A			Likely benign (Jun 01, 2023)
4-99654081-G-T			Likely benign (Mar 01, 2022)
4-99654265-G-A			Benign (Feb 01, 2023)
4-99654634-A-T			Benign (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C4orf54	protein_coding	protein_coding	ENST00000511828	1	18120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.30e-9	1.00	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	829	1.07e+3	0.774	0.0000656	11481
Missense in Polyphen		237	320.15	0.74029		3456
Synonymous	4.22	337	451	0.747	0.0000292	3856
Loss of Function	3.28	21	44.7	0.470	0.00000242	523

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

• ghis: 0.465

Mouse Genome Informatics

• Gene name: 1110002E22Rik