PHTF2

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			87 clinvar	4 clinvar		91
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	94	5	0	99

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 82 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395272.1	RefSeq	NP_001382201.1	18	MANE Select
ENST00000422959.8	Ensembl	ENSP00000403042.2	18	MANE Select
NM_001127357.2	RefSeq	NP_001120829.1	18	Standard
NM_001127358.2	RefSeq	NP_001120830.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

DNA binding

Cellular Component

nucleus
endoplasmic reticulum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000416283
Coding exons: 18
Length: 158697
Individuals with no LoFs: 124604
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 124636
p: 0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.29	243	366	0.663	0.0000182	4874
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00019	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00023	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.000071	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.984

Gene Damage Prediction

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