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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	0

Variants in PHTF2

This is a list of pathogenic ClinVar variants found in the PHTF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-77840260-C-T		not specified	Uncertain significance (Dec 08, 2023)
7-77840280-A-G		not specified	Uncertain significance (Sep 20, 2023)
7-77893631-A-G		not specified	Uncertain significance (Jun 12, 2023)
7-77901854-C-T		not specified	Uncertain significance (Nov 03, 2023)
7-77901866-C-G		not specified	Uncertain significance (Mar 13, 2023)
7-77908807-T-G		not specified	Uncertain significance (Jun 17, 2022)
7-77908930-C-T		not specified	Uncertain significance (Aug 02, 2021)
7-77910258-G-A		not specified	Uncertain significance (Feb 13, 2023)
7-77910315-C-A		not specified	Uncertain significance (Dec 27, 2023)
7-77910360-G-A		not specified	Uncertain significance (Sep 29, 2023)
7-77910372-T-G		not specified	Uncertain significance (Jan 03, 2024)
7-77920343-G-A		not specified	Uncertain significance (Jan 09, 2024)
7-77920356-C-A		not specified	Uncertain significance (Apr 15, 2024)
7-77920367-G-A		not specified	Likely benign (Mar 16, 2022)
7-77920413-G-A		not specified	Likely benign (Oct 12, 2021)
7-77922705-A-G		not specified	Uncertain significance (Dec 18, 2023)
7-77922720-C-G		not specified	Uncertain significance (Aug 22, 2023)
7-77922731-C-T		not specified	Uncertain significance (Jan 03, 2024)
7-77922753-A-G		not specified	Uncertain significance (Aug 01, 2022)
7-77922765-A-G		not specified	Uncertain significance (Apr 13, 2023)
7-77929133-T-C		not specified	Uncertain significance (Apr 08, 2024)
7-77929137-G-C		not specified	Uncertain significance (Mar 11, 2022)
7-77929143-G-A		not specified	Uncertain significance (Mar 28, 2024)
7-77929152-G-A		not specified	Uncertain significance (Nov 17, 2023)
7-77929155-C-G		not specified	Uncertain significance (Aug 28, 2023)

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