PINX1

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

Basic information

Region (hg38): 8:10764960-10839884

Links

ENSG00000254093 ∙ NCBI:54984 ∙ OMIM:606505 ∙ HGNC:30046 ∙ Uniprot:Q96BK5 ∙ 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 PINX1 gene.

• Inborn genetic diseases (29 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PINX1 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			26	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	1

Variants in PINX1

This is a list of pathogenic ClinVar variants found in the PINX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-10765415-T-C		not specified	Uncertain significance (Apr 12, 2023)
8-10765425-C-G		not specified	Uncertain significance (Jan 02, 2024)
8-10765477-T-G		not specified	Uncertain significance (Oct 27, 2023)
8-10765498-C-G		not specified	Uncertain significance (Dec 27, 2022)
8-10765521-G-T		not specified	Uncertain significance (Aug 21, 2023)
8-10765532-C-T		not specified	Uncertain significance (Dec 06, 2022)
8-10765540-G-A		not specified	Uncertain significance (Feb 28, 2023)
8-10765573-G-A		not specified	Likely benign (Dec 15, 2022)
8-10765619-C-G		not specified	Uncertain significance (Dec 18, 2023)
8-10765621-G-A		not specified	Uncertain significance (Dec 23, 2022)
8-10765624-G-A		not specified	Uncertain significance (Dec 23, 2022)
8-10765624-G-C		not specified	Likely benign (May 28, 2023)
8-10765625-C-T		not specified	Uncertain significance (Feb 23, 2023)
8-10765626-G-T		not specified	Likely benign (Feb 21, 2024)
8-10765655-C-A		not specified	Uncertain significance (May 18, 2023)
8-10765655-C-T		not specified	Uncertain significance (Jul 05, 2023)
8-10765658-C-T		not specified	Likely benign (May 03, 2023)
8-10765677-C-G		not specified	Uncertain significance (Dec 21, 2023)
8-10765678-T-C		not specified	Uncertain significance (Dec 21, 2023)
8-10765681-G-A		not specified	Likely benign (Dec 19, 2023)
8-10765683-G-C		not specified	Uncertain significance (Dec 15, 2023)
8-10765700-G-T		not specified	Uncertain significance (Jul 05, 2023)
8-10765704-G-C			Benign (Aug 20, 2018)
8-10765720-T-A		not specified	Uncertain significance (Jun 29, 2023)
8-10765789-G-C		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PINX1	protein_coding	protein_coding	ENST00000314787	7	74922

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.60e-9	0.0614	124540	1	95	124636	0.000385

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.59	280	182	1.54	0.0000106	2154
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000484	0.000480
Ashkenazi Jewish	0.00	0.00
East Asian	0.000298	0.000278
Finnish	0.00223	0.00223
European (Non-Finnish)	0.000153	0.000150
Middle Eastern	0.000298	0.000278
South Asian	0.0000717	0.0000654
Other	0.00183	0.00165

dbNSFP

Source: dbNSFP