SIMC1

SUMO interacting motifs containing 1

Basic information

Region (hg38): 5:176238367-176345991

Previous symbols: [ "C5orf25" ]

Links

ENSG00000170085 ∙ NCBI:375484 ∙ OMIM:618102 ∙ HGNC:24779 ∙ Uniprot:Q8NDZ2 ∙ 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 SIMC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIMC1 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	2
missense			46	2		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	3	1

Variants in SIMC1

This is a list of pathogenic ClinVar variants found in the SIMC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-176238533-G-A		not specified	Uncertain significance (Jul 13, 2022)
5-176238543-G-A		not specified	Uncertain significance (Sep 08, 2024)
5-176238547-T-A			Likely benign (Jan 01, 2023)
5-176238564-C-A		not specified	Uncertain significance (Mar 08, 2024)
5-176238567-G-T		not specified	Uncertain significance (Jun 26, 2024)
5-176238605-C-G		not specified	Uncertain significance (Jun 27, 2022)
5-176295030-A-G		not specified	Uncertain significance (Oct 07, 2024)
5-176295036-G-T		not specified	Uncertain significance (Jul 14, 2024)
5-176295052-C-G		not specified	Uncertain significance (Jan 03, 2024)
5-176295081-A-G		not specified	Likely benign (Feb 13, 2024)
5-176295082-C-T		not specified	Uncertain significance (Aug 15, 2023)
5-176295098-G-T		not specified	Uncertain significance (May 18, 2022)
5-176295106-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-176295122-G-C		not specified	Uncertain significance (Jan 09, 2025)
5-176295127-T-C		not specified	Uncertain significance (Dec 17, 2024)
5-176295144-C-T		not specified	Uncertain significance (Jun 23, 2023)
5-176295153-T-C		not specified	Uncertain significance (Aug 15, 2023)
5-176295170-C-G		not specified	Uncertain significance (Jul 19, 2022)
5-176296267-G-A		not specified	Uncertain significance (Feb 13, 2024)
5-176313724-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-176313733-G-A		not specified	Uncertain significance (Sep 30, 2024)
5-176313751-G-T		not specified	Uncertain significance (Oct 11, 2024)
5-176313808-A-G		not specified	Uncertain significance (Oct 08, 2024)
5-176313810-G-A		not specified	Uncertain significance (May 14, 2024)
5-176313811-G-A		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIMC1	protein_coding	protein_coding	ENST00000341199	9	107630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000392	0.954	125539	0	53	125592	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.536	202	225	0.899	0.0000116	2979
Missense in Polyphen		67	84.982	0.7884		1091
Synonymous	0.0846	85	86.0	0.988	0.00000467	884
Loss of Function	1.87	12	21.3	0.563	0.00000114	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000398	0.000397
Middle Eastern	0.00	0.00
South Asian	0.0000985	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0820

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.59

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.170
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Simc1

Gene ontology

• Molecular function: SUMO polymer binding