MYPOP

protein-coding

Myb related transcription factor, partner of profilin, the group of Myb/SANT domain containing

Gene summary

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001012643.4

Inheritance

—

ClinVar variants

U:79B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr19:45,890,023-45,902,613

External References & Databases

Ensembl (ENSG00000176182)

Transcript & Mutation Effects

hg38 • Region Span ~12.6 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 MYPOP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 78

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001012643.4. 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			2 clinvar			2
missense			77 clinvar	1 clinvar		78
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	1	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001012643.4	RefSeq	NP_001012661.1	2	MANE Select
ENST00000322217.6	Ensembl	ENSP00000325402.4	2	MANE Select
ENST00000904793.1	Ensembl	ENSP00000574852.1	2	Standard
ENST00000904794.1	Ensembl	ENSP00000574853.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
protein homodimerization activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000322217
Coding exons: 2
Length: 12585
Individuals with no LoFs: 123060
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 123063
p: 0.0000122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.975	156	194	0.803	0.0000116	2390
Missense (PolyPhen)		54	85.339	0.63277		967
Synonymous	-0.0401	88	87.5	1.01	0.00000551	921
Loss of Function	2.27	1	7.88	0.127	4.06e-7	106

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000064	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00011	0.00010	rare
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: Transcriptional repressor; DNA-binding protein that specifically recognizes the core sequence 5'-YAAC[GT]G-3'. Dimerization with PFN1 reduces its DNA-binding capacity (By similarity). {ECO:0000250}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.109

Gene Damage Prediction

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