SURF2

surfeit 2

Basic information

Region (hg38): 9:133356550-133361158

Links

ENSG00000148291 ∙ NCBI:6835 ∙ OMIM:185630 ∙ HGNC:11475 ∙ Uniprot:Q15527 ∙ 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 SURF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SURF2 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			17	2	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3		3
Total	0	0	17	6	1

Variants in SURF2

This is a list of pathogenic ClinVar variants found in the SURF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133356570-G-C			Likely benign (Aug 03, 2018)
9-133356606-C-T		not specified	Uncertain significance (Jan 12, 2024)
9-133356635-C-T			Likely benign (Jun 16, 2021)
9-133356636-A-C		not specified	Uncertain significance (Apr 19, 2023)
9-133356661-C-T			Likely benign (Jun 26, 2018)
9-133356665-C-T			Benign (Jun 28, 2018)
9-133356666-G-A		not specified	Uncertain significance (Mar 25, 2024)
9-133356715-T-C			Likely benign (Oct 07, 2019)
9-133356757-CAGGGGAG-C			Likely benign (Sep 26, 2019)
9-133356924-T-A		not specified	Uncertain significance (May 20, 2024)
9-133356957-C-G		not specified	Uncertain significance (Jul 02, 2024)
9-133356999-T-C		not specified	Uncertain significance (Oct 09, 2024)
9-133357017-C-A		not specified	Uncertain significance (Dec 07, 2024)
9-133357033-G-C		not specified	Uncertain significance (Jul 09, 2024)
9-133357733-A-G		not specified	Uncertain significance (Aug 10, 2024)
9-133357770-T-C		not specified	Uncertain significance (Dec 14, 2021)
9-133357779-C-G		not specified	Uncertain significance (Dec 28, 2022)
9-133357791-G-A		not specified	Uncertain significance (Feb 17, 2023)
9-133357809-G-A		not specified	Uncertain significance (Jan 05, 2022)
9-133359950-A-C		not specified	Uncertain significance (Dec 07, 2021)
9-133359973-G-A		not specified	Uncertain significance (May 10, 2024)
9-133359998-T-C		not specified	Uncertain significance (Nov 07, 2024)
9-133360003-C-T		not specified	Uncertain significance (May 30, 2023)
9-133360004-G-A		not specified	Uncertain significance (Oct 27, 2022)
9-133360028-T-A		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SURF2	protein_coding	protein_coding	ENST00000371964	6	4618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000693	0.496	125668	0	39	125707	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.07	183	147	1.25	0.00000860	1649
Missense in Polyphen		68	52.311	1.2999		660
Synonymous	-1.04	71	60.7	1.17	0.00000350	488
Loss of Function	0.645	9	11.3	0.793	6.57e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000368	0.000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.893
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.177
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.774

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Surf2

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;nucleus;nucleolus;plasma membrane;nuclear speck
• Molecular function: molecular_function