C19orf25

chromosome 19 open reading frame 25

Basic information

Region (hg38): 19:1461143-1479219

Links

ENSG00000119559 ∙ NCBI:148223 ∙ ∙ HGNC:26711 ∙ Uniprot:Q9UFG5 ∙ 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 C19orf25 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C19orf25 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			1			1
non coding	2	3	333	209	32	579
Total	2	3	335	209	32

Variants in C19orf25

This is a list of pathogenic ClinVar variants found in the C19orf25 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1461150-C-A			Likely benign (Dec 04, 2023)
19-1461154-G-C		APC2-related disorder	Likely pathogenic (Jan 05, 2024)
19-1461157-G-A			Uncertain significance (Mar 11, 2023)
19-1461163-C-T			Likely benign (Jan 22, 2024)
19-1461170-C-T			Likely benign (Dec 01, 2023)
19-1461171-G-A			Likely benign (Dec 20, 2023)
19-1461949-C-T			Likely benign (Jan 08, 2024)
19-1461955-T-A			Uncertain significance (Dec 18, 2020)
19-1461956-C-T			Likely benign (Apr 16, 2018)
19-1461981-G-A			Uncertain significance (Mar 29, 2022)
19-1461990-G-A			Uncertain significance (Oct 21, 2022)
19-1461995-G-A			Likely benign (Sep 24, 2022)
19-1462006-C-G		Inborn genetic diseases	Uncertain significance (Aug 23, 2021)
19-1462015-GCA-G			Pathogenic (Sep 06, 2023)
19-1462030-C-T			Uncertain significance (Jul 07, 2022)
19-1462052-C-T			Likely benign (Jan 09, 2024)
19-1462053-G-A		Inborn genetic diseases	Uncertain significance (Mar 23, 2022)
19-1462063-TC-T			Pathogenic (Jul 30, 2022)
19-1462067-G-C		APC2-related disorder	Likely benign (Jan 22, 2024)
19-1462084-A-G		not specified	Uncertain significance (Dec 14, 2023)
19-1462102-C-T		See cases • Intellectual developmental disorder, autosomal recessive 74	Uncertain significance (Jul 30, 2024)
19-1462108-C-T		Inborn genetic diseases	Uncertain significance (May 20, 2024)
19-1462109-C-T		APC2-related disorder	Likely benign (Dec 11, 2023)
19-1462115-C-G			Uncertain significance (Feb 21, 2023)
19-1462115-C-T			Likely benign (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C19orf25	protein_coding	protein_coding	ENST00000436106	2	18414

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.403	0.479	114233	0	3	114236	0.0000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.222	75	69.8	1.07	0.00000426	725
Missense in Polyphen		18	19.433	0.92626		228
Synonymous	-0.720	38	32.8	1.16	0.00000216	256
Loss of Function	0.966	0	1.09	0.00	4.58e-8	16

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	0.000107	0.000102
European (Non-Finnish)	0.0000103	0.00000973
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0877

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: 2310011J03Rik

Gene ontology

• Molecular function: protein binding