SCML2

Scm polycomb group protein like 2, the group of MBT domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): X:18239312-18354688

Links

ENSG00000102098 ∙ NCBI:10389 ∙ OMIM:300208 ∙ HGNC:10581 ∙ Uniprot:Q9UQR0 ∙ 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 SCML2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCML2 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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	3	0

Variants in SCML2

This is a list of pathogenic ClinVar variants found in the SCML2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-18246675-C-T		not specified	Likely benign (May 24, 2023)
X-18256860-T-C		not specified	Uncertain significance (Jan 18, 2022)
X-18256934-T-C		not specified	Uncertain significance (Oct 05, 2021)
X-18257008-A-C		not specified	Uncertain significance (Feb 16, 2023)
X-18258051-C-T			Likely benign (Sep 01, 2022)
X-18258073-G-C		not specified	Uncertain significance (Dec 17, 2023)
X-18258157-G-C		not specified	Uncertain significance (Feb 17, 2024)
X-18260224-C-T		not specified	Uncertain significance (Oct 06, 2022)
X-18260228-G-A		not specified	Uncertain significance (Aug 02, 2023)
X-18265730-G-A		not specified	Uncertain significance (Sep 06, 2022)
X-18265733-G-A		not specified	Uncertain significance (Jun 01, 2023)
X-18265758-C-T		not specified	Likely benign (Aug 13, 2021)
X-18305088-G-A		not specified	Uncertain significance (Jul 19, 2023)
X-18305106-C-T		not specified	Uncertain significance (Mar 01, 2023)
X-18324029-T-C		not specified	Uncertain significance (Apr 13, 2022)
X-18330619-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCML2	protein_coding	protein_coding	ENST00000251900	14	115414

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000387	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.40	149	257	0.579	0.0000190	4588
Missense in Polyphen		29	92.053	0.31503		1594
Synonymous	1.69	73	93.8	0.778	0.00000698	1362
Loss of Function	4.40	0	22.6	0.00	0.00000168	410

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0950

Intolerance Scores

• loftool: 0.135
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.128
• hipred: Y
• hipred_score: 0.627
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.487

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scml2
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;anatomical structure morphogenesis
• Cellular component: nucleus;PcG protein complex
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding