IFTAP

protein-coding

intraflagellar transport associated protein

Gene summary

This gene encodes a protein that was identified as a cellular interacting partner of non-structural protein 10 of the severe acute respiratory syndrome coronavirus (SARS-CoV). The encoded protein may function as a negative regulator of transcription. There is a pseudogene for this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]

Previous symbols:

C11orf74

MANE transcript

NM_138787.4

Inheritance

—

ClinVar variants

U:7

Top phenotype

Histiocytic medullary reticulosis

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr11:36,594,369-36,675,695

External References & Databases

Ensembl (ENSG00000166352)

Transcript & Mutation Effects

hg38 • Region Span ~81.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IFTAP variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 4

Histiocytic medullary reticulosisTotal: 2

Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positiveTotal: 2

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138787.4. Only rare variants are included.

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						0
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	7	0	0	7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138787.4	RefSeq	NP_620142.2	5	MANE Select
ENST00000334307.10	Ensembl	ENSP00000334848.5	5	MANE Select
NM_001276722.2	RefSeq	NP_001263651.1	5	Standard
NM_001276723.2	RefSeq	NP_001263652.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000532470
Coding exons: 5
Length: 78773
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125742
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.186	112	107	1.05	0.00000474	1485
Missense (PolyPhen)		29	24.602	1.1788		389
Synonymous	-0.0884	37	36.3	1.02	0.00000165	371
Loss of Function	0.142	8	8.45	0.947	3.55e-7	119

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00010	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0735

Intolerance Scores

LoFtool: 0.391
RVIS EVS: 0.19
RVIS percentile EVS: 66.82

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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