SURF6

surfeit 6

Basic information

Region (hg38): 9:133328775-133336188

Links

ENSG00000148296 ∙ NCBI:6838 ∙ OMIM:185642 ∙ HGNC:11478 ∙ Uniprot:O75683 ∙ 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 SURF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SURF6 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	0

Variants in SURF6

This is a list of pathogenic ClinVar variants found in the SURF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133331930-A-C		not specified	Uncertain significance (Jan 03, 2022)
9-133332015-C-T		not specified	Uncertain significance (May 02, 2024)
9-133332032-T-A		not specified	Uncertain significance (Oct 22, 2021)
9-133332048-G-A		not specified	Uncertain significance (Sep 14, 2022)
9-133332051-G-C		not specified	Uncertain significance (Feb 12, 2024)
9-133332065-T-G		not specified	Uncertain significance (Mar 17, 2023)
9-133332103-G-C		not specified	Uncertain significance (Oct 04, 2022)
9-133332107-C-T		not specified	Uncertain significance (Jan 19, 2022)
9-133332129-T-C		not specified	Uncertain significance (Jun 07, 2024)
9-133332132-A-G		not specified	Uncertain significance (Sep 22, 2022)
9-133332184-A-T		not specified	Uncertain significance (Aug 13, 2021)
9-133332561-A-G		not specified	Uncertain significance (Oct 02, 2023)
9-133332570-G-A		not specified	Uncertain significance (Apr 20, 2024)
9-133332579-G-A		not specified	Uncertain significance (Jun 10, 2022)
9-133332598-C-T		not specified	Uncertain significance (Dec 21, 2022)
9-133332678-C-T		not specified	Uncertain significance (Jan 10, 2023)
9-133332688-T-C		not specified	Uncertain significance (Feb 22, 2023)
9-133332693-C-T		not specified	Uncertain significance (May 24, 2023)
9-133332717-C-T		not specified	Uncertain significance (Apr 28, 2022)
9-133332733-C-T		not specified	Likely benign (Aug 09, 2021)
9-133332741-G-A		not specified	Uncertain significance (Nov 13, 2023)
9-133333722-C-A		not specified	Uncertain significance (Nov 02, 2021)
9-133333725-C-T		not specified	Uncertain significance (Jun 13, 2024)
9-133333737-A-T		not specified	Uncertain significance (Dec 05, 2022)
9-133333797-G-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SURF6	protein_coding	protein_coding	ENST00000372022	5	5684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.45e-7	0.704	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.273	253	241	1.05	0.0000174	2265
Missense in Polyphen		65	60.072	1.082		536
Synonymous	-1.75	126	103	1.22	0.00000685	749
Loss of Function	1.18	12	17.3	0.694	0.00000107	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000385
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000332	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000239	0.000229
Middle Eastern	0.000332	0.000326
South Asian	0.000556	0.000523
Other	0.000986	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to both DNA and RNA in vitro, with a stronger binding capacity for RNA. May represent a nucleolar constitutive protein involved in ribosomal biosynthesis or assembly (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.710
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.28

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.471
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.761

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Surf6

Zebrafish Information Network

• Gene name: surf6
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: ribosomal large subunit biogenesis;ribosomal small subunit biogenesis
• Cellular component: granular component;nucleoplasm;nucleolus;cytosolic large ribosomal subunit
• Molecular function: DNA binding;RNA binding;protein binding