SERF2

small EDRK-rich factor 2

Basic information

Region (hg38): 15:43777087-43804427

Links

ENSG00000140264 ∙ NCBI:10169 ∙ OMIM:605054 ∙ HGNC:10757 ∙ Uniprot:P84101 ∙ 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 SERF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERF2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in SERF2

This is a list of pathogenic ClinVar variants found in the SERF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43793647-C-G		not specified	Uncertain significance (Mar 13, 2023)
15-43793767-C-T		not specified	Uncertain significance (May 04, 2022)
15-43793809-C-T		not specified	Uncertain significance (Nov 21, 2023)
15-43793815-T-C		not specified	Uncertain significance (Dec 27, 2023)
15-43793821-G-C		not specified	Uncertain significance (Oct 06, 2021)
15-43793823-G-A		not specified	Uncertain significance (Oct 06, 2022)
15-43793946-C-A		not specified	Uncertain significance (Dec 28, 2022)
15-43800605-C-T		not specified	Uncertain significance (Nov 17, 2022)
15-43800606-G-A		not specified	Uncertain significance (Nov 10, 2022)
15-43800612-G-A		not specified	Uncertain significance (Sep 22, 2023)
15-43800634-G-C		not specified	Uncertain significance (Apr 26, 2023)
15-43800635-G-A		not specified	Uncertain significance (Jun 02, 2023)
15-43800641-G-A		not specified	Uncertain significance (Oct 13, 2023)
15-43800658-G-A			Benign (May 16, 2018)
15-43800666-C-T		not specified	Uncertain significance (Dec 15, 2022)
15-43801560-G-A			Benign (May 16, 2018)
15-43801711-A-G		not specified	Uncertain significance (Aug 16, 2022)
15-43801716-T-C			Benign (May 16, 2018)
15-43801735-G-A		not specified	Uncertain significance (May 21, 2024)
15-43801793-C-T		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERF2	protein_coding	protein_coding	ENST00000409960	3	25503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0232	0.783	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.227	95	101	0.937	0.00000536	1078
Missense in Polyphen		3	7.278	0.4122		72
Synonymous	0.919	34	41.5	0.819	0.00000246	376
Loss of Function	0.947	3	5.37	0.559	2.40e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000425	0.000425
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Haploinsufficiency Scores

• pHI: 0.242
• hipred: N
• hipred_score: 0.146
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.764

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serf2

Gene ontology

• Biological process: biological_process
• Cellular component: nucleus;cytosol
• Molecular function: molecular_function