SCML4

protein-coding

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

Gene summary

Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198081.5

Inheritance

—

ClinVar variants

U:61B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr6:107,702,154-107,824,317

External References & Databases

Ensembl (ENSG00000146285)

Transcript & Mutation Effects

hg38 • Region Span ~122.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCML4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198081.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			60 clinvar	1 clinvar	1 clinvar	62
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	61	1	2	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198081.5	RefSeq	NP_932347.2	7	MANE Select
ENST00000369020.8	Ensembl	ENSP00000358016.3	7	MANE Select
NM_001286408.2	RefSeq	NP_001273337.1	6	Standard
NM_001286409.2	RefSeq	NP_001273338.1	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
scml4	Danio rerio	Structure: definitive hemopoiesis Quality: decreased occurrence abnormal

Gene / Model

Organism

Observed Phenotype

scml4

Danio rerio

Structure: definitive hemopoiesis

Quality: decreased occurrence

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369020
Coding exons: 7
Length: 120214
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125747
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.683	218	248	0.878	0.0000148	2663
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.649

Gene Damage Prediction

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