SUMF2

sulfatase modifying factor 2

Basic information

Region (hg38): 7:56064001-56080670

Links

ENSG00000129103 ∙ NCBI:25870 ∙ OMIM:607940 ∙ HGNC:20415 ∙ Uniprot:Q8NBJ7 ∙ 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 SUMF2 gene.

• Inborn genetic diseases (27 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUMF2 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			21	2		23
nonsense			1	1		2
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	27	4	1

Variants in SUMF2

This is a list of pathogenic ClinVar variants found in the SUMF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-56064263-G-T		SUMF2-related disorder	Likely benign (Apr 30, 2019)
7-56064264-C-T		not specified	Uncertain significance (Aug 09, 2021)
7-56064283-G-A		not specified	Uncertain significance (May 03, 2023)
7-56064300-G-T		not specified	Uncertain significance (Aug 04, 2021)
7-56064318-C-T		not specified	Uncertain significance (Sep 22, 2021)
7-56064322-A-C		not specified	Uncertain significance (May 18, 2022)
7-56064339-C-G		not specified	Uncertain significance (Mar 01, 2024)
7-56064343-T-G		not specified	Uncertain significance (Jan 08, 2024)
7-56064346-T-C		not specified	Uncertain significance (Jan 26, 2022)
7-56064358-T-C		not specified	Uncertain significance (Jan 09, 2024)
7-56064368-G-C		not specified	Uncertain significance (Aug 04, 2023)
7-56068490-C-T			Uncertain significance (Jul 02, 2021)
7-56068577-C-T			Uncertain significance (Jul 02, 2021)
7-56068584-C-T		not specified	Likely benign (Jan 26, 2022)
7-56068616-C-T		not specified	Uncertain significance (Nov 10, 2022)
7-56068623-C-A		not specified	Uncertain significance (May 24, 2023)
7-56073026-C-A		not specified	Uncertain significance (Jun 09, 2022)
7-56073066-CTT-C			Benign (Feb 04, 2019)
7-56073095-C-T		not specified	Uncertain significance (Feb 05, 2024)
7-56074613-G-A		not specified	Uncertain significance (Jun 23, 2023)
7-56074625-C-T		not specified	Uncertain significance (Dec 19, 2022)
7-56074629-C-T		not specified	Uncertain significance (Feb 14, 2023)
7-56074677-G-A		not specified	Uncertain significance (May 09, 2022)
7-56074702-A-C		not specified	Uncertain significance (Apr 25, 2022)
7-56074722-G-A		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUMF2	protein_coding	protein_coding	ENST00000342190	8	16669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.97e-9	0.316	125096	12	639	125747	0.00259

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.526	223	202	1.10	0.0000105	2284
Missense in Polyphen		64	56.038	1.1421		628
Synonymous	-0.355	88	83.9	1.05	0.00000464	727
Loss of Function	0.695	14	17.1	0.819	8.92e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0370	0.0368
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.00	0.00
South Asian	0.000133	0.000131
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lacks formylglycine generating activity and is unable to convert newly synthesized inactive sulfatases to their active form. Inhibits the activation of sulfatases by SUMF1. {ECO:0000269|PubMed:12757706, ECO:0000269|PubMed:15708861, ECO:0000269|PubMed:15962010}.
• Pathway: Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;The activation of arylsulfatases;Gamma carboxylation, hypusine formation and arylsulfatase activation;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.687

Intolerance Scores

• loftool: 0.0730
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.0718
• hipred: N
• hipred_score: 0.112
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sumf2

Gene ontology

• Biological process: glycosphingolipid metabolic process;post-translational protein modification
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: metal ion binding