Is IL17RC p.Pro699= (c.2097G>C) pathogenic?

IL17RC p.Pro699= (c.2097G>C) is classified Likely benign in IL17RC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-13). Very rare (popmax 0.00896%, eas); Associated with candidiasis, familial, 9.

What condition is associated with IL17RC p.Pro699= (c.2097G>C)?

IL17RC p.Pro699= (c.2097G>C) is associated with candidiasis, familial, 9 (ClinVar).

How common is IL17RC p.Pro699= (c.2097G>C) in the general population?

IL17RC p.Pro699= (c.2097G>C) is very rare (popmax 0.00896%, eas) (gnomAD).

How is Chronic mucocutaneous candidiasis inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

IL17RC p.Pro699=

c.2097G>C · VCV3717386

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00896%, eas)

Conditions

candidiasis, familial, 9

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.2	GERP -2.2
Overall
CADD	3.932	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00896% East Asian · 4/44,642 alleles

Filtering AF 0.00299% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00181%

Overall 0.00131% 19/1,454,836 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00896%	11,161
European (non-Finnish)	0.00127%	78,488

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: IL17RC
Protein: p.Pro699=
Coding: c.2097G>C
MANE Select: NM_153460
Type: single nucleotide variant
Location: chr3:9933527 (GRCh38)
Gene constraint: LOEUF 0.777 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.19 · 5 PDB
Residue 699: the sefir domain

Full IL17RC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

candidiasis, familial, 9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Chronic mucocutaneous candidiasis (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Childhood, Infancy

Similar variants

IL17RC p.Pro699Leu Uncertain significance ★ ⚠ same residue
IL17RC p.Pro699Ser Uncertain significance ★ ⚠ same residue
IL17RC c.105+146G>A Uncertain significance ★★ ⚠ same condition
IL17RC c.105+25G>A Uncertain significance ★★ ⚠ same condition
IL17RC c.105+33G>T Uncertain significance ★★ ⚠ same condition
IL17RC c.106-144G>A Uncertain significance ★★ ⚠ same condition
IL17RC p.Ala166Val Uncertain significance ★★ ⚠ same condition
IL17RC p.Ala30Ser Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/il17rc-p-pro699 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown