SCML4

Scm polycomb group protein like 4, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 6:107702153-107824317

Links

ENSG00000146285 ∙ NCBI:256380 ∙ ∙ HGNC:21397 ∙ Uniprot:Q8N228 ∙ 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 SCML4 gene.

• Inborn genetic diseases (15 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCML4 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			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	2

Variants in SCML4

This is a list of pathogenic ClinVar variants found in the SCML4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-107705250-C-T		not specified	Uncertain significance (Oct 25, 2023)
6-107705274-A-G		not specified	Uncertain significance (Jul 05, 2023)
6-107705289-C-A		not specified	Uncertain significance (May 08, 2023)
6-107705321-A-G		not specified	Uncertain significance (Dec 14, 2022)
6-107707929-C-T			Benign (Jul 16, 2018)
6-107707975-C-T		not specified	Uncertain significance (Mar 01, 2023)
6-107707990-G-A			Benign (Apr 26, 2018)
6-107720729-G-A		not specified	Uncertain significance (Jun 02, 2023)
6-107720805-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-107720897-G-A		not specified	Uncertain significance (Jan 02, 2024)
6-107744976-C-T		not specified	Uncertain significance (Apr 28, 2022)
6-107745084-C-T		not specified	Uncertain significance (Sep 16, 2021)
6-107746713-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-107746724-A-T		not specified	Uncertain significance (May 27, 2022)
6-107746749-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-107746811-A-C		not specified	Uncertain significance (Dec 08, 2021)
6-107749747-G-C		not specified	Uncertain significance (Jan 26, 2022)
6-107749761-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-107749811-G-C		not specified	Uncertain significance (Jan 22, 2024)
6-107772272-G-A		not specified	Uncertain significance (Jun 11, 2021)
6-107772308-G-A		not specified	Uncertain significance (Jan 27, 2022)
6-107772308-G-C		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCML4	protein_coding	protein_coding	ENST00000369020	7	120214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000759	0.919	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	218	248	0.878	0.0000148	2663
Missense in Polyphen		44	57.918	0.7597		688
Synonymous	0.372	104	109	0.955	0.00000730	867
Loss of Function	1.66	11	18.8	0.586	0.00000113	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000110	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000110	0.000109
South Asian	0.0000327	0.0000327
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}.

Intolerance Scores

• loftool: 0.520
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.426
• hipred: N
• hipred_score: 0.219
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.649

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scml4

Zebrafish Information Network

• Gene name: scml4
• Affected structure: definitive hemopoiesis
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Cellular component: nucleoplasm