PKD1L1-AS1

PKD1L1 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 7:47795291-47819847

Previous symbols: [ "C7orf69" ]

Links

ENSG00000136275 ∙ NCBI:80099 ∙ ∙ HGNC:21911 ∙ Uniprot:Q9H7B7 ∙ 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 PKD1L1-AS1 gene.

• not provided (51 variants)
• Inborn genetic diseases (26 variants)
• Heterotaxy, visceral, 8, autosomal (10 variants)
• PKD1L1-related condition (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKD1L1-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	5	2	38	9	31	85
Total	5	2	38	9	31

Highest pathogenic variant AF is 0.0000658

Variants in PKD1L1-AS1

This is a list of pathogenic ClinVar variants found in the PKD1L1-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
7-47795989-G-A			Uncertain significance (Jan 22, 2024)
7-47796002-A-G		PKD1L1-related disorder	Uncertain significance (Apr 04, 2024)
7-47796019-C-A		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
7-47796098-T-G		Inborn genetic diseases	Uncertain significance (Jul 26, 2021)
7-47796123-G-T		PKD1L1-related disorder	Uncertain significance (Jul 08, 2024)
7-47796135-T-C		Inborn genetic diseases	Uncertain significance (Dec 09, 2023)
7-47796153-A-G		PKD1L1-related disorder	Likely benign (Dec 04, 2021)
7-47796216-G-A			Benign (Jun 19, 2021)
7-47800486-C-T			Benign (Nov 12, 2018)
7-47800503-G-A			Benign (Jun 20, 2021)
7-47800686-A-T		PKD1L1-related disorder	Uncertain significance (Sep 12, 2024)
7-47800698-C-A		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
7-47800704-A-G		Inborn genetic diseases	Uncertain significance (Oct 24, 2023)
7-47800709-C-A		PKD1L1-related disorder	Likely benign (Feb 04, 2022)
7-47800710-C-T		PKD1L1-related disorder • Heterotaxy, visceral, 8, autosomal	Uncertain significance (Jan 19, 2024)
7-47800711-G-A		PKD1L1-related disorder	Uncertain significance (Jan 30, 2023)
7-47800712-C-G		PKD1L1-related disorder	Benign (Jan 20, 2024)
7-47800719-G-C		Inborn genetic diseases	Uncertain significance (May 09, 2023)
7-47800736-GAGGCAGTCTT-G		Heterotaxy, visceral, 8, autosomal	Pathogenic (Jul 24, 2023)
7-47800738-G-A		Inborn genetic diseases • PKD1L1-related disorder	Likely benign (Jan 03, 2024)
7-47800739-G-T			Pathogenic (Jul 05, 2022)
7-47800780-C-T		Inborn genetic diseases	Uncertain significance (Sep 29, 2023)
7-47800781-G-A		PKD1L1-related disorder	Benign (Oct 10, 2023)
7-47800783-G-A		Heterotaxy, visceral, 8, autosomal	Uncertain significance (Dec 02, 2021)
7-47800789-C-T		Heterotaxy, visceral, 8, autosomal	Benign (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKD1L1-AS1	protein_coding	protein_coding	ENST00000258776	3	24557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00166	0.479	123506	0	35	123541	0.000142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0462	56	57.0	0.983	0.00000243	801
Missense in Polyphen		3	2.0068	1.4949		25
Synonymous	-0.545	22	19.0	1.16	8.18e-7	214
Loss of Function	0.0227	4	4.05	0.988	1.71e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00191	0.00191
Finnish	0.00	0.00
European (Non-Finnish)	0.00000889	0.00000889
Middle Eastern	0.00191	0.00191
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.598
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.04

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Cellular component: extracellular region