PHF13

Chr 1

PHD finger protein 13

Also known as: PHF5, SPOC1

NCBI Gene: 148479 ENSG00000116273 UniProt: Q86YI8 OMIM: 620054

PHF13 encodes a chromatin-binding protein that regulates chromosome condensation during mitosis and modulates DNA damage response by recruiting corepressors and histone methyltransferases. The gene is highly constrained against loss-of-function variants (pLI 0.98, LOEUF 0.25), but specific disease associations and inheritance patterns have not yet been established in humans. Based on functional studies, mutations would likely affect cell division and chromatin regulation processes.

OMIM ResearchSummary from RefSeq, UniProt

Enables chromatin binding activity; chromatin-protein adaptor activity; and methylated histone binding activity. Involved in mitotic chromosome condensation and regulation of DNA repair. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.25

Clinical Summary— PHF13

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

36 VUS of 48 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.25LOEUF

pLI 0.980

Z-score 3.21

OE 0.00 (0.00–0.25)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.76Z-score

OE missense 0.64 (0.56–0.75)

124 obs / 192.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.25)

0≤0.351.4

Missense OE?0.64 (0.56–0.75)

0≤0.61.4

Synonymous OE?1.26

0≤1.21.6

LoF obs/exp: 0 / 12.0Missense obs/exp: 124 / 192.8Syn Z: -1.88

This gene — mechanism propensity

0.3196th %ile

GOF

0.2298th %ile

LOF

0.83top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.25

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

48 submitted variants in ClinVar

ClinVar

Classification Summary

VUS36

Likely Benign3

Benign2

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	36	0	0	36
Likely Benign	3	0	0	3
Benign	0	1	1	2
Total	39	1	1	41

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

55 pathogenic / likely-pathogenic (of 64) ClinVar copy-number / structural variants overlap PHF13 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →