ANKS6

ankyrin repeat and sterile alpha motif domain containing 6, the group of Ankyrin repeat domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 9:98731329-98796965

Previous symbols: [ "SAMD6", "ANKRD14" ]

Links

ENSG00000165138 ∙ NCBI:203286 ∙ OMIM:615370 ∙ HGNC:26724 ∙ Uniprot:Q68DC2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephronophthisis 16 (Definitive), mode of inheritance: AR
• nephronophthisis 16 (Strong), mode of inheritance: AR
• nephronophthisis 2 (Supportive), mode of inheritance: AR
• nephronophthisis 1 (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephronophthisis 16	AR	Cardiovascular	Individuals have been described with congenital heart anomalies, and awareness may enable early diagnosis and management	Cardiovascular; Gastrointestinal; Renal	23793029
Renal transplant has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANKS6 gene.

• Nephronophthisis_16 (423 variants)
• Inborn_genetic_diseases (155 variants)
• not_provided (113 variants)
• ANKS6-related_disorder (23 variants)
• not_specified (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKS6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173551.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	118	2	125
missense		4	303	24	4	335
nonsense	5	5	3			13
start loss						0
frameshift	13	5	2			20
splice donor/acceptor (+/-2bp)	2	2	6			10
Total	20	16	319	142	6

Highest pathogenic variant AF is 0.00003965918

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKS6	protein_coding	protein_coding	ENST00000353234	15	65637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124731	0	66	124797	0.000264

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0756	463	458	1.01	0.0000279	5561
Missense in Polyphen		130	147.33	0.88238		1742
Synonymous	0.121	199	201	0.989	0.0000139	1865
Loss of Function	2.89	14	31.5	0.444	0.00000168	380

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000356	0.000356
Ashkenazi Jewish	0.0000998	0.0000993
East Asian	0.000115	0.000111
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000279	0.000274
Middle Eastern	0.000115	0.000111
South Asian	0.000643	0.000588
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for renal function. {ECO:0000269|PubMed:23793029}.
• Disease: DISEASE: Nephronophthisis 16 (NPHP16) [MIM:615382]: A form of nephronophthisis, a chronic tubulo-interstitial nephritis that progresses to end-stage renal failure. Some patients have cystic kidneys of normal size and no extrarenal manifestations, whereas others have enlarged renal size and severe extrarenal defects, including hypertrophic obstructive cardiomyopathy, aortic stenosis, pulmonary stenosis, patent ductus arteriosus, situs inversus, and periportal liver fibrosis. {ECO:0000269|PubMed:23793029}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.678
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.59

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.339

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoplasm;cilium
• Molecular function: protein binding