SEL1L3

SEL1L family member 3

Basic information

Region (hg38): 4:25747432-25863760

Links

ENSG00000091490 ∙ NCBI:23231 ∙ OMIM:619914 ∙ HGNC:29108 ∙ Uniprot:Q68CR1 ∙ 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 SEL1L3 gene.

• Inborn genetic diseases (44 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEL1L3 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					2	2
missense			40	4	5	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	40	4	7

Variants in SEL1L3

This is a list of pathogenic ClinVar variants found in the SEL1L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-25748441-G-A		not specified	Likely benign (Jul 07, 2022)
4-25748462-T-G		not specified	Uncertain significance (Jan 21, 2022)
4-25748517-T-C		not specified	Likely benign (Feb 16, 2023)
4-25748522-G-A		not specified	Uncertain significance (Dec 27, 2022)
4-25757558-C-T		not specified	Uncertain significance (Dec 21, 2022)
4-25757698-T-C		not specified	Uncertain significance (Jan 24, 2023)
4-25757712-C-G			Benign (Apr 16, 2018)
4-25757722-C-T		not specified	Uncertain significance (Dec 04, 2021)
4-25758986-G-A		not specified	Uncertain significance (Jun 29, 2023)
4-25759003-G-T		not specified	Uncertain significance (Mar 24, 2023)
4-25759041-C-T		not specified	Uncertain significance (Feb 14, 2023)
4-25776286-T-G		not specified	Uncertain significance (Jun 29, 2023)
4-25776328-T-A		not specified	Uncertain significance (Jul 12, 2023)
4-25776329-A-G		not specified	Uncertain significance (Jun 07, 2023)
4-25782384-T-A		not specified	Uncertain significance (Nov 18, 2022)
4-25788280-C-T		not specified	Uncertain significance (Feb 27, 2024)
4-25788337-C-A		not specified	Uncertain significance (Aug 12, 2021)
4-25788360-C-T		not specified	Uncertain significance (Mar 20, 2023)
4-25790562-T-C			Benign (Jun 21, 2018)
4-25790571-A-G		not specified	Uncertain significance (Feb 10, 2022)
4-25802299-G-A		not specified	Uncertain significance (Aug 31, 2022)
4-25802375-T-G		not specified	Uncertain significance (Jun 06, 2023)
4-25804723-C-G		not specified	Uncertain significance (Mar 01, 2023)
4-25804727-T-C			Benign (Jun 21, 2018)
4-25804749-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEL1L3	protein_coding	protein_coding	ENST00000399878	24	116328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00358	0.996	124545	0	96	124641	0.000385

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	495	583	0.849	0.0000310	7333
Missense in Polyphen		138	208.3	0.6625		2577
Synonymous	1.35	198	224	0.885	0.0000127	2140
Loss of Function	5.26	17	61.5	0.277	0.00000302	761

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00100	0.000992
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000167
Finnish	0.00233	0.00232
European (Non-Finnish)	0.000187	0.000186
Middle Eastern	0.000169	0.000167
South Asian	0.0000654	0.0000654
Other	0.000498	0.000495

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.671
• rvis_EVS: -0.13
• rvis_percentile_EVS: 44.09

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.400
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sel1l3

Gene ontology

• Cellular component: nucleus;nucleoplasm;integral component of membrane