PHF13

PHD finger protein 13, the group of PHD finger proteins

Basic information

Region (hg38): 1:6613731-6624030

Links

ENSG00000116273 ∙ NCBI:148479 ∙ OMIM:620054 ∙ HGNC:22983 ∙ Uniprot:Q86YI8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PHF13 gene.

• not_specified (30 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153812.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	1	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF13	protein_coding	protein_coding	ENST00000377648	4	10349

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.980	0.0196	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	124	193	0.643	0.0000130	1979
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.646
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.647

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf13
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: mitotic cell cycle;chromatin organization;chromosome segregation;mitotic chromosome condensation;cell division
• Cellular component: nucleus;nucleoplasm
• Molecular function: chromatin binding;methylated histone binding;metal ion binding