PHTF1

putative homeodomain transcription factor 1

Basic information

Region (hg38): 1:113696830-113759489

Previous symbols: [ "PHTF" ]

Links

ENSG00000116793 ∙ NCBI:10745 ∙ OMIM:604950 ∙ HGNC:8939 ∙ Uniprot:Q9UMS5 ∙ 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 PHTF1 gene.

• Inborn genetic diseases (32 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHTF1 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				1		1
missense			32			32
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in PHTF1

This is a list of pathogenic ClinVar variants found in the PHTF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-113698291-T-C		not specified	Uncertain significance (Feb 28, 2023)
1-113698333-T-G		not specified	Uncertain significance (Aug 17, 2022)
1-113698344-G-T		not specified	Uncertain significance (Dec 08, 2023)
1-113699735-T-C		not specified	Uncertain significance (Nov 29, 2023)
1-113699763-T-C		not specified	Uncertain significance (Jan 30, 2024)
1-113699769-G-A		not specified	Uncertain significance (Oct 26, 2022)
1-113700819-T-C		not specified	Uncertain significance (Dec 06, 2022)
1-113700862-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-113700866-T-TA			Uncertain significance (Dec 18, 2017)
1-113704680-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-113704743-T-C		not specified	Uncertain significance (Oct 29, 2021)
1-113705913-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-113705932-C-A		not specified	Uncertain significance (Oct 04, 2022)
1-113705941-A-C			Likely benign (Sep 01, 2022)
1-113705988-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-113706003-C-A		not specified	Uncertain significance (Nov 10, 2021)
1-113706008-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-113706036-A-C		not specified	Uncertain significance (May 13, 2022)
1-113706059-C-A		not specified	Uncertain significance (Jun 24, 2022)
1-113706063-T-C		not specified	Uncertain significance (Oct 06, 2021)
1-113706068-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-113706071-A-G		not specified	Uncertain significance (Jun 22, 2021)
1-113706077-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-113706114-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-113706118-A-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHTF1	protein_coding	protein_coding	ENST00000369604	18	62659

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.69e-26	0.00170	125464	0	284	125748	0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	345	403	0.857	0.0000208	4974
Missense in Polyphen		104	139.07	0.74785		1850
Synonymous	0.743	124	135	0.919	0.00000654	1428
Loss of Function	0.603	41	45.4	0.903	0.00000250	542

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00205	0.00204
Ashkenazi Jewish	0.00505	0.00497
East Asian	0.000768	0.000761
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000958	0.000941
Middle Eastern	0.000768	0.000761
South Asian	0.00180	0.00177
Other	0.00133	0.00130

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.271
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.93

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.282
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phtf1

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus;endoplasmic reticulum;cis-Golgi network
• Molecular function: DNA binding;DNA-binding transcription factor activity