MORF4L2

protein-coding

mortality factor 4 like 2, the group of EMSY complex

Gene summary

Involved in positive regulation of double-strand break repair via homologous recombination and regulation of cell cycle. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_012286.3

Inheritance

—

ClinVar variants

U:24

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:103,675,496-103,688,158

External References & Databases

Ensembl (ENSG00000123562)

Transcript & Mutation Effects

hg38 • Region Span ~12.7 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 MORF4L2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012286.3. 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						0
missense			24 clinvar			24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	0	0	24

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 196 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012286.3	RefSeq	NP_036418.1	1	MANE Select
ENST00000441076.7	Ensembl	ENSP00000391969.2	1	MANE Select
NM_001142418.2	RefSeq	NP_001135890.1	1	Standard
NM_001142419.2	RefSeq	NP_001135891.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chromatin modifying enzymes
HATs acetylate histones
Chromatin organization

Biological Process

DNA repair
chromatin silencing
histone acetylation
histone deacetylation
regulation of growth

Molecular Function

protein binding

Cellular Component

histone acetyltransferase complex
nucleus
nucleoplasm
nucleolus
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000423833
Coding exons: 1
Length: 12663
Individuals with no LoFs: 124753
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124754
p: 0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.76	56	107	0.521	0.00000798	1876
Missense (PolyPhen)		5	16.823	0.29721		358
Synonymous	0.703	36	41.8	0.862	0.00000320	565
Loss of Function	2.17	0	5.50	0.00	3.45e-7	128

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000037	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histone H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senescence, apoptosis, and DNA repair. The NuA4 complex ATPase and helicase activities seem to be, at least in part, contributed by the association of RUVBL1 and RUVBL2 with EP400. NuA4 may also play a direct role in DNA repair when directly recruited to sites of DNA damage. Also component of the MSIN3A complex which acts to repress transcription by deacetylation of nucleosomal histones.;

Recessive Scores

pRec: 0.0955

Intolerance Scores

RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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