SIM2

SIM bHLH transcription factor 2, the group of Basic helix-loop-helix proteins|PAS domain containing

Basic information

Region (hg38): 21:36699115-36749917

Previous symbols: [ "SIM" ]

Links

ENSG00000159263 ∙ NCBI:6493 ∙ OMIM:600892 ∙ HGNC:10883 ∙ Uniprot:Q14190 ∙ 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 SIM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIM2 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				4	3	7
missense			46	1		47
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	5	3

Variants in SIM2

This is a list of pathogenic ClinVar variants found in the SIM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-36699814-T-C		not specified	Uncertain significance (Oct 05, 2023)
21-36709186-G-A		not specified	Uncertain significance (Dec 15, 2022)
21-36709191-C-A		not specified	Uncertain significance (Sep 17, 2021)
21-36709234-G-A		not specified	Uncertain significance (Apr 07, 2022)
21-36709245-C-G		not specified	Uncertain significance (Jun 29, 2023)
21-36712565-T-A			Likely benign (Apr 01, 2023)
21-36719840-G-A		not specified	Uncertain significance (Mar 16, 2022)
21-36719859-T-C			Benign (Jul 31, 2018)
21-36719872-G-A		not specified	Uncertain significance (Feb 22, 2023)
21-36723048-A-G		Neurodevelopmental with craniofacial anomalies disorder	Likely pathogenic (Dec 08, 2021)
21-36723060-G-A		not specified	Uncertain significance (Oct 26, 2022)
21-36723063-C-T		not specified	Uncertain significance (Oct 06, 2022)
21-36726149-A-G		not specified	Uncertain significance (Jun 07, 2024)
21-36726161-C-A		not specified	Uncertain significance (Jan 04, 2024)
21-36726223-G-A			Benign (Jun 04, 2018)
21-36731052-G-A		not specified	Uncertain significance (Oct 05, 2023)
21-36731059-C-T		not specified	Uncertain significance (Apr 20, 2023)
21-36731106-G-A		not specified	Uncertain significance (Aug 25, 2021)
21-36731121-G-A		not specified	Uncertain significance (May 13, 2024)
21-36741767-C-T		not specified	Uncertain significance (Dec 06, 2022)
21-36741768-G-A		not specified	Uncertain significance (Dec 23, 2022)
21-36741814-C-G		not specified	Uncertain significance (Jan 09, 2024)
21-36741842-G-A		not specified	Uncertain significance (Oct 22, 2021)
21-36743396-A-C		not specified	Uncertain significance (Oct 12, 2022)
21-36743488-G-C		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIM2	protein_coding	protein_coding	ENST00000290399	11	50786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.200	0.800	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.962	268	316	0.848	0.0000182	4237
Missense in Polyphen		85	116.03	0.73257		1340
Synonymous	-0.396	152	146	1.04	0.00000984	1373
Loss of Function	3.75	7	28.7	0.244	0.00000147	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000812	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that may be a master gene of CNS development in cooperation with Arnt. It may have pleiotropic effects in the tissues expressed during development.

Recessive Scores

• pRec: 0.247

Intolerance Scores

• loftool: 0.632
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.17

Haploinsufficiency Scores

• pHI: 0.362
• hipred: Y
• hipred_score: 0.758
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sim2
• Phenotype: growth/size/body region phenotype; digestive/alimentary phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;nervous system development;embryonic pattern specification;cell differentiation;lung development
• Cellular component: nucleus;nucleoplasm;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein heterodimerization activity