UBAC2

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

Basic information

Region (hg38): 13:99200773-99386504

Previous symbols: [ "PHGDHL1" ]

Links

ENSG00000134882 ∙ NCBI:337867 ∙ ∙ HGNC:20486 ∙ Uniprot:Q8NBM4 ∙ 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 UBAC2 gene.

• Inborn genetic diseases (33 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBAC2 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				1		1
missense			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			23	2		25
Total	0	0	32	4	1

Variants in UBAC2

This is a list of pathogenic ClinVar variants found in the UBAC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-99238469-C-T		not specified	Uncertain significance (Feb 09, 2023)
13-99238471-C-T			Benign (Apr 07, 2018)
13-99238486-G-A		not specified	Uncertain significance (Jun 22, 2023)
13-99238518-T-C		not specified	Likely benign (Nov 17, 2023)
13-99238529-T-C		not specified	Uncertain significance (Jan 08, 2024)
13-99243846-A-G		not specified	Uncertain significance (Jan 10, 2022)
13-99244567-T-C		not specified	Uncertain significance (May 16, 2023)
13-99254885-T-G		not specified	Uncertain significance (Apr 28, 2023)
13-99254926-C-A		not specified	Uncertain significance (Aug 28, 2023)
13-99254941-C-A		not specified	Uncertain significance (Dec 01, 2022)
13-99254970-C-T		not specified	Uncertain significance (Jun 28, 2022)
13-99254986-C-T		not specified	Uncertain significance (Dec 16, 2023)
13-99255034-C-G		not specified	Uncertain significance (Feb 13, 2024)
13-99255079-T-A		not specified	Uncertain significance (Oct 06, 2021)
13-99255182-T-G		not specified	Uncertain significance (Dec 18, 2023)
13-99255217-G-A		not specified	Uncertain significance (Oct 27, 2022)
13-99255224-C-T		not specified	Uncertain significance (Feb 23, 2023)
13-99255245-T-C		not specified	Uncertain significance (Jun 24, 2022)
13-99255314-G-T			Likely benign (Jul 29, 2018)
13-99255430-A-G		not specified	Uncertain significance (Jul 15, 2021)
13-99255446-C-T		not specified	Uncertain significance (Oct 04, 2022)
13-99255452-C-G		not specified	Uncertain significance (Nov 08, 2022)
13-99255542-G-A		not specified	Uncertain significance (Jan 09, 2024)
13-99255655-A-G		not specified	Uncertain significance (Nov 30, 2021)
13-99255657-T-C		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBAC2	protein_coding	protein_coding	ENST00000403766	9	185661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00626	0.990	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	126	186	0.676	0.0000101	2239
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000877	0.0000877
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000441	0.000435
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.000441	0.000435
South Asian	0.000132	0.000131
Other	0.000165	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.792
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubac2

Gene ontology

• Biological process: protein localization to endoplasmic reticulum;negative regulation of retrograde protein transport, ER to cytosol
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding