CCDC115

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				9 clinvar	1 clinvar	10
missense	1 clinvar		24 clinvar	3 clinvar	1 clinvar	29
nonsense			2 clinvar			2
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	2	0	26	12	2	42

Highest pathogenic variant AF is 0.0000460981

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 0 of 0 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
No transcripts match your selected source or search query.

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular iron ion homeostasis
lysosomal lumen acidification
cellular response to increased oxygen levels
vacuolar proton-transporting V-type ATPase complex assembly
lysosomal protein catabolic process

Molecular Function

unfolded protein binding

Cellular Component

lysosome
endosome
endoplasmic reticulum
endoplasmic reticulum-Golgi intermediate compartment
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259229
Coding exons: 5
Length: 4109
Individuals with no LoFs: 125696
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125747
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.109	106	109	0.971	0.00000588	1133
Missense (PolyPhen)		38	33.56	1.1323		363
Synonymous	-0.261	46	43.8	1.05	0.00000203	385
Loss of Function	-0.332	10	8.93	1.12	3.90e-7	95

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.00085	0.00085	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Accessory component of the proton-transporting vacuolar (V)-ATPase protein pump involved in intracellular iron homeostasis. In aerobic conditions, required for intracellular iron homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent proteasomal degradation. Necessary for endolysosomal acidification and lysosomal degradation (PubMed:28296633). May be involved in Golgi homeostasis (PubMed:26833332). {ECO:0000269|PubMed:26833332, ECO:0000269|PubMed:28296633}.;

Recessive Scores

pRec: 0.0994

Intolerance Scores

LoFtool: 0.436
RVIS EVS: -0.25
RVIS percentile EVS: 35.42

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.262

Gene Damage Prediction

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