YIPF5

Yip1 domain family member 5, the group of Yip1 domain containing

Basic information

Region (hg38): 5:144158161-144170714

Links

ENSG00000145817 ∙ NCBI:81555 ∙ OMIM:611483 ∙ HGNC:24877 ∙ Uniprot:Q969M3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary microcephaly-epilepsy-permanent neonatal diabetes syndrome (Supportive), mode of inheritance: AR
• microcephaly, epilepsy, and diabetes syndrome 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly, epilepsy, and diabetes syndrome 2	AR	Endocrine	Among other findings, individuals have been described with neonatal-onset, insulin-requiring diabetes mellitus, and awareness may allow prompt recognition and medical management	Endocrine; Neurologic	33164986

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the YIPF5 gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)
• Microcephaly, epilepsy, and diabetes syndrome 2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIPF5 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			7		2	9
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	9	0	2

Variants in YIPF5

This is a list of pathogenic ClinVar variants found in the YIPF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-144160405-C-T			Benign (Feb 01, 2024)
5-144160438-C-T		not specified	Uncertain significance (Nov 02, 2023)
5-144160519-A-T		Microcephaly, epilepsy, and diabetes syndrome 2	Pathogenic (Apr 16, 2021)
5-144160536-G-T		not specified	Uncertain significance (Oct 26, 2022)
5-144160557-C-T		not specified	Uncertain significance (Jan 24, 2024)
5-144162251-A-G		not specified	Uncertain significance (Jan 17, 2024)
5-144162287-G-A		Microcephaly, epilepsy, and diabetes syndrome 2	Pathogenic (Apr 16, 2021)
5-144162293-C-A		not specified	Uncertain significance (Mar 01, 2023)
5-144162305-A-T		Microcephaly, epilepsy, and diabetes syndrome 2	Uncertain significance (Sep 16, 2022)
5-144162314-A-G		not specified	Uncertain significance (Mar 14, 2023)
5-144164176-T-C		not specified	Uncertain significance (Jun 11, 2021)
5-144164212-C-T		not specified	Uncertain significance (Oct 17, 2023)
5-144164220-GTTT-G		Microcephaly, epilepsy, and diabetes syndrome 2	Pathogenic (Apr 16, 2021)
5-144164237-G-C		not specified	Uncertain significance (Jan 23, 2023)
5-144164247-A-C		Microcephaly, epilepsy, and diabetes syndrome 2	Pathogenic (Apr 16, 2021)
5-144164250-C-A		Microcephaly, epilepsy, and diabetes syndrome 2	Pathogenic (Apr 16, 2021)
5-144165488-G-A			Benign (Mar 01, 2024)
5-144165558-G-C		not specified	Uncertain significance (Nov 03, 2023)
5-144165564-C-T		not specified	Uncertain significance (Apr 25, 2022)
5-144165581-G-C		not specified	Uncertain significance (May 11, 2022)
5-144169897-T-C		not specified	Uncertain significance (Feb 15, 2023)
5-144169948-C-A		not specified	Uncertain significance (Jan 30, 2024)
5-144169955-T-C			Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIPF5	protein_coding	protein_coding	ENST00000274496	5	12556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0147	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	112	134	0.835	0.00000615	1664
Missense in Polyphen		12	32.191	0.37278		401
Synonymous	1.25	40	51.4	0.778	0.00000279	487
Loss of Function	3.31	0	12.8	0.00	5.38e-7	169

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

• Function: FUNCTION: Plays a role in transport between endoplasmic reticulum and Golgi. {ECO:0000269|PubMed:11489904, ECO:0000269|PubMed:15611160}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.110
• hipred: Y
• hipred_score: 0.595
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yipf5
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: protein transport;vesicle-mediated transport;regulation of ER to Golgi vesicle-mediated transport
• Cellular component: nucleoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane;COPII-coated ER to Golgi transport vesicle;intracellular membrane-bounded organelle;endoplasmic reticulum exit site
• Molecular function: protein binding