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GeneBe

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

ENSG00000102098NCBI:10389OMIM:300208HGNC:10581Uniprot:Q9UQR0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCML2 gene.

  • Inborn genetic diseases (10 variants)
  • not provided (1 variants)

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
clinvar
1
missense
8
clinvar
2
clinvar
10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 8 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)2520012
X-18256860-T-C not specified Uncertain significance (Jan 18, 2022)2271861
X-18256934-T-C not specified Uncertain significance (Oct 05, 2021)2341924
X-18257008-A-C not specified Uncertain significance (Feb 16, 2023)2485753
X-18258051-C-T Likely benign (Sep 01, 2022)2660099
X-18258073-G-C not specified Uncertain significance (Dec 17, 2023)3158480
X-18258157-G-C not specified Uncertain significance (Feb 17, 2024)3158479
X-18260224-C-T not specified Uncertain significance (Oct 06, 2022)2317246
X-18260228-G-A not specified Uncertain significance (Aug 02, 2023)2615276
X-18265730-G-A not specified Uncertain significance (Sep 06, 2022)3158483
X-18265733-G-A not specified Uncertain significance (Jun 01, 2023)2554815
X-18265758-C-T not specified Likely benign (Aug 13, 2021)2380439
X-18305088-G-A not specified Uncertain significance (Jul 19, 2023)2603406
X-18305106-C-T not specified Uncertain significance (Mar 01, 2023)2492944
X-18324029-T-C not specified Uncertain significance (Apr 13, 2022)3158481
X-18330619-G-A not specified Uncertain significance (Dec 28, 2023)3158482

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCML2protein_codingprotein_codingENST00000251900 14115414
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00038700000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.401492570.5790.00001904588
Missense in Polyphen2992.0530.315031594
Synonymous1.697393.80.7780.000006981362
Loss of Function4.40022.60.000.00000168410

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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