UBAC2

protein-coding

UBA domain containing 2, the group of MicroRNA protein coding host genes|Rhomboid family

Gene summary

Predicted to enable serine-type endopeptidase activity. Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PHGDHL1

MANE transcript

NM_001144072.2

Inheritance

—

ClinVar variants

U:57B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr13:99,200,774-99,386,504

External References & Databases

Ensembl (ENSG00000134882)

Transcript & Mutation Effects

hg38 • Region Span ~185.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UBAC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 139

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001144072.2. 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			2 clinvar	5 clinvar		7
missense			45 clinvar	2 clinvar	1 clinvar	48
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	57	7	1	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001144072.2	RefSeq	NP_001137544.1	9	MANE Select
ENST00000403766.8	Ensembl	ENSP00000383911.3	9	MANE Select
NM_177967.4	RefSeq	NP_808882.1	7	Standard
ENST00000355700.9	Ensembl	ENSP00000347928.5	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein localization to endoplasmic reticulum
negative regulation of retrograde protein transport, ER to cytosol

Molecular Function

protein binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000403766
Coding exons: 9
Length: 185661
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125748
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.57	126	186	0.676	0.0000101	2239
Missense (PolyPhen)		16	43.961	0.36396		527
Synonymous	0.708	65	72.7	0.894	0.00000433	669
Loss of Function	2.53	7	18.9	0.371	9.84e-7	216

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00044	0.00044	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Restricts trafficking of FAF2 from the endoplasmic reticulum to lipid droplets. {ECO:0000269|PubMed:23297223}.;

Recessive Scores

pRec: 0.123

Intolerance Scores

LoFtool: 0.372
RVIS EVS: -0.52
RVIS percentile EVS: 21.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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