SCML1

Scm polycomb group protein like 1, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): X:17737448-17754988

Links

ENSG00000047634 ∙ NCBI:6322 ∙ OMIM:300227 ∙ HGNC:10580 ∙ Uniprot:Q9UN30 ∙ 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 SCML1 gene.

• not provided (2 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCML1 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					1	1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	1	1	1

Variants in SCML1

This is a list of pathogenic ClinVar variants found in the SCML1 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-17745535-A-G		not specified	Uncertain significance (Dec 16, 2023)
X-17746051-A-G		not specified	Uncertain significance (Jul 08, 2022)
X-17749482-C-T			Benign (Dec 31, 2019)
X-17750159-A-G		not specified	Uncertain significance (Dec 15, 2022)
X-17751942-T-G			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCML1	protein_coding	protein_coding	ENST00000380041	7	17518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0372	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	56	128	0.437	0.0000104	2148
Missense in Polyphen		4	32.813	0.1219		585
Synonymous	1.13	43	53.5	0.804	0.00000470	633
Loss of Function	2.97	0	10.3	0.00	7.91e-7	185

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. May be involved in spermatogenesis during sexual maturation (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0673

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.0265
• hipred: N
• hipred_score: 0.380
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00277

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

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