SURF4

surfeit 4

Basic information

Region (hg38): 9:133361450-133376166

Links

ENSG00000148248 ∙ NCBI:6836 ∙ OMIM:185660 ∙ HGNC:11476 ∙ Uniprot:O15260 ∙ 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 SURF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SURF4 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in SURF4

This is a list of pathogenic ClinVar variants found in the SURF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133363519-T-C		not specified	Uncertain significance (Aug 07, 2023)
9-133363630-T-C		not specified	Uncertain significance (Nov 18, 2022)
9-133363644-T-C		not specified	Uncertain significance (Oct 14, 2023)
9-133363654-C-A		not specified	Uncertain significance (Oct 24, 2024)
9-133364847-A-C		not specified	Uncertain significance (Jun 09, 2022)
9-133364854-C-T		not specified	Uncertain significance (Feb 19, 2025)
9-133364871-G-A		not specified	Uncertain significance (Jun 06, 2023)
9-133364940-A-G		not specified	Uncertain significance (Jan 03, 2025)
9-133364950-C-T			Uncertain significance (Feb 08, 2023)
9-133364979-C-T		not specified	Uncertain significance (Sep 20, 2023)
9-133366004-C-T		not specified	Uncertain significance (Jan 31, 2023)
9-133366637-A-G		not specified	Uncertain significance (Jan 21, 2025)
9-133367310-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-133367348-C-A		not specified	Uncertain significance (Dec 13, 2022)
9-133367438-C-A		not specified	Uncertain significance (Nov 02, 2023)
9-133367439-G-A		not specified	Uncertain significance (Mar 01, 2024)
9-133375962-T-C		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SURF4	protein_coding	protein_coding	ENST00000371989	6	14646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.606	0.393	125705	0	2	125707	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	82	156	0.525	0.00000951	1770
Missense in Polyphen		21	67.125	0.31285		778
Synonymous	0.488	61	66.0	0.924	0.00000465	528
Loss of Function	2.60	2	11.5	0.173	4.92e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the maintenance of the architecture of the endoplasmic reticulum-Golgi intermediate compartment and of the Golgi. {ECO:0000269|PubMed:18287528}.
• Pathway: Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.126
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.367
• hipred: Y
• hipred_score: 0.662
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Surf4

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi organization;positive regulation of organelle organization;protein exit from endoplasmic reticulum;early endosome to Golgi transport;neutrophil degranulation
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;cytosol;plasma membrane;integral component of membrane;transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane;azurophil granule membrane
• Molecular function: protein binding