PHF13

protein-coding

PHD finger protein 13, the group of PHD finger proteins

Gene summary

Enables chromatin binding activity and histone H3K9me2/3 reader activity. Involved in DNA damage response and mitotic chromosome condensation. Located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_153812.3

Inheritance

—

ClinVar variants

U:41B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr1:6,613,731-6,624,030

External References & Databases

Ensembl (ENSG00000116273)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 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 PHF13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153812.3. 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			1 clinvar		1 clinvar	2
missense			37 clinvar	3 clinvar		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	41	3	1	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153812.3	RefSeq	NP_722519.2	4	MANE Select
ENST00000377648.5	Ensembl	ENSP00000366876.4	4	MANE Select
ENST00000961800.1	Ensembl	ENSP00000631859.1	3	Standard
ENST00000961800.2	Ensembl	ENSP00000631859.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitotic cell cycle
chromatin organization
chromosome segregation
mitotic chromosome condensation
cell division

Molecular Function

chromatin binding
methylated histone binding
metal ion binding

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377648
Coding exons: 4
Length: 10349
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.76	124	193	0.643	0.0000130	1979
Missense (PolyPhen)		25	78.074	0.32021		759
Synonymous	-1.88	103	81.5	1.26	0.00000560	589
Loss of Function	3.21	0	12.0	0.00	6.80e-7	138

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
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: Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis. {ECO:0000269|PubMed:19638409}.;

Recessive Scores

pRec: 0.121

Intolerance Scores

RVIS EVS: -0.43
RVIS percentile EVS: 25.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.647

Gene Damage Prediction

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