SURF2

protein-coding

surfeit 2

Gene summary

This gene shares a bidirectional promoter with surfeit 1 (SURF1; GeneID: 6834), which is located on the opposite strand. It encodes a conserved protein that is expressed in a variety of tissues. [provided by RefSeq, Jul 2013]

MANE transcript

NM_017503.5

Inheritance

—

ClinVar variants

U:65B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr9:133,356,550-133,361,158

External References & Databases

Ensembl (ENSG00000148291)

Transcript & Mutation Effects

hg38 • Region Span ~4.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SURF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 62

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017503.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			62 clinvar	2 clinvar		64
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	65	4	0	69

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017503.5	RefSeq	NP_059973.4	6	MANE Select
ENST00000371964.5	Ensembl	ENSP00000361032.4	6	MANE Select
NM_001278928.2	RefSeq	NP_001265857.1	6	Standard
ENST00000875735.1	Ensembl	ENSP00000545794.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component
nucleus
nucleolus
plasma membrane
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371964
Coding exons: 6
Length: 4618
Individuals with no LoFs: 125668
Homozygous LoFs: 0
Heterozygous LoFs: 39
Defined: 125707
p: 0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.07	183	147	1.25	0.00000860	1649
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.893
RVIS EVS: 0.62
RVIS percentile EVS: 83.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.774

Gene Damage Prediction

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