PHTF2

putative homeodomain transcription factor 2

Basic information

Region (hg38): 7:77798773-77957503

Links

ENSG00000006576 ∙ NCBI:57157 ∙ OMIM:616785 ∙ HGNC:13411 ∙ Uniprot:Q8N3S3 ∙ 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 PHTF2 gene.

• not_specified (76 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHTF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001395272.1. 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						0
missense			72	4		76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHTF2	protein_coding	protein_coding	ENST00000416283	18	158697

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000177	1.00	124604	0	32	124636	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	243	366	0.663	0.0000182	4874
Missense in Polyphen		69	157.53	0.438		2166
Synonymous	1.15	108	124	0.869	0.00000614	1429
Loss of Function	3.83	14	40.2	0.348	0.00000219	516

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000345	0.000340
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000226	0.000223
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000140	0.000133
Middle Eastern	0.000226	0.000223
South Asian	0.0000709	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in transcription regulation.

Recessive Scores

• pRec: 0.0995

Intolerance Scores

• loftool: 0.142
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.476
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phtf2
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

• Cellular component: nucleus;endoplasmic reticulum
• Molecular function: DNA binding