YIPF3

Yip1 domain family member 3, the group of Yip1 domain containing

Basic information

Region (hg38): 6:43511831-43516985

Previous symbols: [ "C6orf109" ]

Links

ENSG00000137207 ∙ NCBI:25844 ∙ OMIM:609775 ∙ HGNC:21023 ∙ Uniprot:Q9GZM5 ∙ 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 YIPF3 gene.

• Inborn genetic diseases (15 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIPF3 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				2		2
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	1	4
Total	0	0	15	6	1

Variants in YIPF3

This is a list of pathogenic ClinVar variants found in the YIPF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43512193-C-A		not specified	Uncertain significance (Feb 21, 2024)
6-43512196-C-T		not specified	Uncertain significance (Dec 09, 2023)
6-43512208-C-T		not specified	Uncertain significance (Jan 20, 2023)
6-43512287-G-T		not specified	Uncertain significance (Jun 02, 2023)
6-43512457-T-C		not specified	Uncertain significance (Oct 13, 2021)
6-43512539-C-T		not specified	Uncertain significance (Oct 26, 2021)
6-43512544-C-T		not specified	Uncertain significance (Jul 14, 2021)
6-43512765-C-T		not specified	Uncertain significance (Oct 05, 2021)
6-43512831-T-C		not specified	Uncertain significance (Jun 06, 2023)
6-43513095-T-A		not specified	Uncertain significance (May 17, 2023)
6-43513104-C-T		not specified	Uncertain significance (Apr 06, 2023)
6-43513593-G-A		not specified	Uncertain significance (Nov 08, 2022)
6-43513620-T-C		not specified	Uncertain significance (Sep 12, 2023)
6-43515971-G-A		not specified	Uncertain significance (Aug 02, 2023)
6-43515978-C-T		not specified	Uncertain significance (Jan 10, 2023)
6-43516003-G-A			Likely benign (Oct 01, 2021)
6-43516009-G-A			Likely benign (Jan 01, 2023)
6-43516758-G-T		not specified	Uncertain significance (Feb 09, 2022)
6-43516761-C-A		not specified	Uncertain significance (May 24, 2023)
6-43516794-G-A			Likely benign (Jul 14, 2018)
6-43516856-G-A			Likely benign (Jul 14, 2018)
6-43516856-G-T			Likely benign (Jul 06, 2018)
6-43516878-C-T			Likely benign (Jul 06, 2018)
6-43516905-G-A			Benign (Jul 09, 2018)
6-43516985-C-CGGG			Likely benign (Oct 02, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIPF3	protein_coding	protein_coding	ENST00000372422	9	5164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.141	0.858	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.625	186	212	0.879	0.0000117	2248
Missense in Polyphen		47	66.67	0.70497		710
Synonymous	-0.763	94	85.0	1.11	0.00000495	730
Loss of Function	2.95	5	18.8	0.266	9.87e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000631	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maintenance of the Golgi structure. May play a role in hematopoiesis. {ECO:0000269|PubMed:12490290, ECO:0000269|PubMed:21757827}.

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.450
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.595
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yipf3

Gene ontology

• Biological process: cell differentiation
• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane;transport vesicle;intracellular membrane-bounded organelle
• Molecular function: protein binding