PINX1

protein-coding

PIN2 (TERF1) interacting telomerase inhibitor 1, the group of MicroRNA protein coding host genes|SSU processome|G-patch domain containing

Gene summary

Enables telomerase RNA binding activity and telomerase inhibitor activity. Involved in several processes, including negative regulation of telomere maintenance via telomerase; positive regulation of protein localization to nucleolus; and protein localization to nucleolus. Acts upstream of or within telomere maintenance via telomerase. Located in chromosomal region; nuclear lumen; and spindle. Implicated in hepatocellular carcinoma. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017884.6

Inheritance

—

ClinVar variants

U:91B:10

Top phenotype

Male infertility

gnomAD constraint

pLI —, LoF o/e 1.13

Max pathogenic AF

—

Genomic locus

chr8:10,764,961-10,839,884

External References & Databases

Ensembl (ENSG00000254093)

Transcript & Mutation Effects

hg38 • Region Span ~74.9 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 PINX1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 1

Male infertilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017884.6. 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			2 clinvar		1 clinvar	3
missense			85 clinvar	9 clinvar		94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	91	9	1	101

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017884.6	RefSeq	NP_060354.4	7	MANE Select
ENST00000314787.8	Ensembl	ENSP00000318966.3	7	MANE Select
NM_001284356.2	RefSeq	NP_001271285.1	6	Standard
ENST00000519088.5	Ensembl	ENSP00000428853.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314787
Coding exons: 7
Length: 74922
Individuals with no LoFs: 124540
Homozygous LoFs: 1
Heterozygous LoFs: 95
Defined: 124636
p: 0.000385

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.59	280	182	1.54	0.0000106	2154
Missense (PolyPhen)		46	36.282	1.2679		498
Synonymous	-2.28	94	69.8	1.35	0.00000449	585
Loss of Function	-0.400	12	10.6	1.13	4.58e-7	129

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00030	0.00028	rare
Finnish	0.0022	0.0022	notable
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.000072	0.000065	rare
Other	0.0018	0.0017	notable