SEL1L2

SEL1L2 adaptor subunit of ERAD E3 ubiquitin ligase

Basic information

Region (hg38): 20:13849246-13996443

Previous symbols: [ "C20orf50" ]

Links

ENSG00000101251 ∙ NCBI:80343 ∙ OMIM:614289 ∙ HGNC:15897 ∙ Uniprot:Q5TEA6 ∙ 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 SEL1L2 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEL1L2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in SEL1L2

This is a list of pathogenic ClinVar variants found in the SEL1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-13850263-G-A			Likely benign (Jun 01, 2022)
20-13995758-G-A		MACROD2-related disorder	Benign (May 28, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEL1L2	protein_coding	protein_coding	ENST00000378072	18	147197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.34e-20	0.0135	124698	0	98	124796	0.000393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.267	279	292	0.956	0.0000144	3756
Missense in Polyphen		102	116.5	0.87551		1514
Synonymous	0.924	98	110	0.888	0.00000636	1016
Loss of Function	0.670	32	36.4	0.880	0.00000169	484

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000960	0.000910
Ashkenazi Jewish	0.000304	0.000298
East Asian	0.000223	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000393	0.000388
Middle Eastern	0.000223	0.000223
South Asian	0.000859	0.000850
Other	0.000550	0.000495

dbNSFP

Source: dbNSFP

• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0744

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0353

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sel1l2

Gene ontology

• Cellular component: integral component of membrane