PITX1-AS1

PITX1 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 5:135033280-135358219

Previous symbols: [ "C5orf66" ]

Links

ENSG00000224186 ∙ NCBI:100996485 ∙ ∙ HGNC:48332 ∙ ∙ ∙ 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 PITX1-AS1 gene.

• not provided (9 variants)
• Inborn genetic diseases (4 variants)
• Talipes equinovarus (2 variants)
• not specified (1 variants)
• PITX1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PITX1-AS1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	9	2	5	17
Total	0	1	9	2	5

Variants in PITX1-AS1

This is a list of pathogenic ClinVar variants found in the PITX1-AS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-135033568-G-A			Benign (May 14, 2021)
5-135033724-G-A		Clubfoot	Uncertain significance (Aug 20, 2021)
5-135033743-C-A			Uncertain significance (Oct 19, 2022)
5-135033793-G-A		not specified	Uncertain significance (May 04, 2022)
5-135033794-CG-C		Clubfoot	Likely pathogenic (Oct 13, 2021)
5-135033803-T-C		not specified	Uncertain significance (Dec 12, 2023)
5-135033805-T-G			Uncertain significance (Mar 19, 2022)
5-135033807-A-G			Likely benign (May 16, 2018)
5-135033813-T-TGGC		PITX1-related disorder	Uncertain significance (Feb 28, 2023)
5-135033815-G-A		not specified	Uncertain significance (Jun 02, 2023)
5-135033846-C-T			Likely benign (Jul 17, 2023)
5-135033862-C-A		not specified	Uncertain significance (Jun 22, 2024)
5-135034102-C-A			Benign (May 14, 2021)
5-135034150-CCCGGCT-C			Benign (May 14, 2021)
5-135034491-C-T			Benign (May 22, 2021)
5-135335028-C-T		not specified	Uncertain significance (Feb 21, 2024)
5-135335067-G-T		not specified	Uncertain significance (Sep 25, 2023)
5-135335071-T-C		not specified	Uncertain significance (Jul 14, 2022)
5-135335080-C-T		not specified	Uncertain significance (Apr 11, 2023)
5-135335100-T-C		not specified	Uncertain significance (Jun 07, 2023)
5-135343265-G-A			Benign (Aug 18, 2018)
5-135343347-A-G		not specified	Uncertain significance (Mar 01, 2023)
5-135343348-G-A		not specified	Uncertain significance (Oct 03, 2022)
5-135343366-C-T		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PITX1-AS1	protein_coding	protein_coding	ENST00000432382	3	322775

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000527	0.471	125409	0	91	125500	0.000363

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	44	74.2	0.593	0.00000391	934
Missense in Polyphen		2	6.3556	0.31468		69
Synonymous	0.136	31	32.0	0.969	0.00000208	285
Loss of Function	0.169	5	5.43	0.922	3.18e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00223	0.00223
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000714	0.000707
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.00	0.00
South Asian	0.000262	0.000261
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153
• ghis: 0.394

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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