YIPF5

protein-coding

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

Gene summary

Involved in insulin processing and regulation of ER to Golgi vesicle-mediated transport. Located in Golgi apparatus and endoplasmic reticulum. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_030799.9

Inheritance

ClinVar variants

P:4U:34B:2

Top phenotype

Microcephaly, epilepsy, and diabetes syndrome 2

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr5:144,158,162-144,170,714

External References & Databases

Ensembl (ENSG00000145817)

Transcript & Mutation Effects

hg38 • Region Span ~12.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

primary microcephaly-epilepsy-permanent neonatal diabetes syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013647

Submitter: Orphanet

microcephaly, epilepsy, and diabetes syndrome 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0025690

Submitter: PanelApp Australia

microcephaly, epilepsy, and diabetes syndrome 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0025690

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Microcephaly, epilepsy, and diabetes syndrome 2AR

Manifestation: Endocrine; Neurologic

Intervention: Endocrine

Rationale: Among other findings, individuals have been described with neonatal-onset, insulin-requiring diabetes mellitus, and awareness may allow prompt recognition and medical management

Refs: 33164986

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to YIPF5 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 32

Microcephaly, epilepsy, and diabetes syndrome 2Total: 6

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030799.9. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense	4 clinvar		32 clinvar		1 clinvar	37
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	4	0	34	1	1	40

Highest pathogenic variant AF is 0.0000020644125

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030799.9	RefSeq	NP_110426.4	5	MANE Select
ENST00000274496.10	Ensembl	ENSP00000274496.5	5	MANE Select
NM_001024947.4	RefSeq	NP_001020118.1	5	Standard
NM_001271732.2	RefSeq	NP_001258661.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
vesicle-mediated transport
regulation of ER to Golgi vesicle-mediated transport

Molecular Function

protein binding

Cellular Component

nucleoplasm
endoplasmic reticulum
endoplasmic reticulum membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000274496
Coding exons: 5
Length: 12556
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.678	112	134	0.835	0.00000615	1664
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.468

Gene Damage Prediction

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