C4orf45

chromosome 4 open reading frame 45

Basic information

Region (hg38): 4:158893133-159038760

Links

ENSG00000164123 ∙ NCBI:152940 ∙ ∙ HGNC:26342 ∙ Uniprot:Q96LM5 ∙ 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 C4orf45 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C4orf45 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	3	0	0

Variants in C4orf45

This is a list of pathogenic ClinVar variants found in the C4orf45 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-158895783-A-G		not specified	Uncertain significance (Apr 25, 2022)
4-158904486-C-T		not specified	Uncertain significance (May 24, 2024)
4-158915303-G-C		not specified	Uncertain significance (Oct 12, 2021)
4-158960298-T-C		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C4orf45	protein_coding	protein_coding	ENST00000434826	5	145627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.37e-7	0.224	124589	0	38	124627	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0888	93	90.6	1.03	0.00000423	1201
Missense in Polyphen		24	28.748	0.83484		376
Synonymous	-0.247	36	34.2	1.05	0.00000188	330
Loss of Function	0.141	10	10.5	0.953	4.43e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000512
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000634	0.0000619
Middle Eastern	0.00	0.00
South Asian	0.000428	0.000425
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.5

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

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: Gm17359
• Phenotype: immune system phenotype; skeleton phenotype; hematopoietic system phenotype