SCMH1

Scm polycomb group protein homolog 1, the group of MBT domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 1:41027201-41242306

Links

ENSG00000010803 ∙ NCBI:22955 ∙ OMIM:616396 ∙ HGNC:19003 ∙ Uniprot:Q96GD3 ∙ 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 SCMH1 gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCMH1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in SCMH1

This is a list of pathogenic ClinVar variants found in the SCMH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-41028216-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-41028318-T-C		not specified	Uncertain significance (Dec 02, 2022)
1-41028702-C-A		not specified	Uncertain significance (Feb 05, 2024)
1-41028707-C-A		not specified	Uncertain significance (Feb 06, 2024)
1-41028720-T-C		not specified	Uncertain significance (Sep 16, 2021)
1-41037372-T-C			Likely benign (Oct 01, 2022)
1-41037397-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-41037412-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-41037427-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-41037482-T-C		not specified	Uncertain significance (Apr 22, 2022)
1-41037509-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-41037541-C-A		not specified	Uncertain significance (Oct 27, 2021)
1-41046422-C-T		not specified	Uncertain significance (Jul 22, 2022)
1-41046443-T-C		not specified	Uncertain significance (Dec 17, 2023)
1-41046461-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-41046492-A-T		not specified	Uncertain significance (May 05, 2023)
1-41046539-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-41048720-T-G		not specified	Uncertain significance (Sep 22, 2022)
1-41048735-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-41048800-C-T		not specified	Uncertain significance (Oct 14, 2023)
1-41070688-C-T		not specified	Likely benign (Oct 03, 2022)
1-41070697-G-C		not specified	Uncertain significance (Jan 29, 2024)
1-41075250-G-C		not specified	Uncertain significance (Apr 26, 2023)
1-41075335-C-T		not specified	Uncertain significance (Mar 22, 2023)
1-41075449-C-A		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCMH1	protein_coding	protein_coding	ENST00000402904	13	214955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000861	0.999	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	285	394	0.723	0.0000229	4310
Missense in Polyphen		111	186.37	0.59559		2102
Synonymous	-0.0134	147	147	1.00	0.00000790	1331
Loss of Function	2.96	14	32.1	0.436	0.00000179	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000179
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with Polycomb group (PcG) multiprotein complexes; the complex class is required to maintain the transcriptionally repressive state of some genes. {ECO:0000250}.
• Pathway: Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;Oxidative Stress Induced Senescence;SUMOylation of DNA damage response and repair proteins;Cellular Senescence;SUMOylation of chromatin organization proteins;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.564
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.14

Haploinsufficiency Scores

• pHI: 0.240
• hipred: Y
• hipred_score: 0.575
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scmh1
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; immune system phenotype; skeleton phenotype; reproductive system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: chromatin remodeling;spermatogenesis;anterior/posterior pattern specification;gene silencing;negative regulation of transcription, DNA-templated
• Cellular component: nucleoplasm;chromocenter
• Molecular function: protein binding