Is CFAP20 p.Leu83Val (c.247C>G) pathogenic?

CFAP20 p.Leu83Val (c.247C>G) is classified Uncertain significance in CFAP20 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-01). AlphaMissense: likely benign (0.1343); Very rare (popmax 0.00668%, eas).

How common is CFAP20 p.Leu83Val (c.247C>G) in the general population?

CFAP20 p.Leu83Val (c.247C>G) is very rare (popmax 0.00668%, eas) (gnomAD).

What do computational predictors say about CFAP20 p.Leu83Val (c.247C>G)?

AlphaMissense predicts likely benign (score 0.1343) — an in-silico prediction, not a clinical call.

CFAP20 p.Leu83Val

c.247C>G · rs1289473219 · VCV2542498

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1343 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1343	likely benign
REVEL	0.233	benign-leaning
SaProt	LLR -10.74	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP -0.08, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 15 kb · p 2.1e-05 · regional, not allelic
Overall
CADD	21.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,882 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.000274% 4/1,460,648 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,961
European (non-Finnish)	8.48e-05%	1,178,921

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: CFAP20
Protein: p.Leu83Val
Coding: c.247C>G
MANE Select: NM_013242
dbSNP: rs1289473219
Type: single nucleotide variant
Location: chr16:58116070 (GRCh38)
Gene constraint: LOEUF 0.783 · pLI 0.07 (gnomAD)
Structure: AlphaFold pLDDT 91.81 · 3 PDB

Full CFAP20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP20 c.164+1G>A Uncertain significance ★ same type
CFAP20 p.Arg101Cys Uncertain significance ★ ⚠ same type
CFAP20 p.Arg113Gln Uncertain significance ★ ⚠ same type
CFAP20 p.Arg113Trp Uncertain significance ★ ⚠ same type
CFAP20 p.Arg161Ser Uncertain significance ★ ⚠ same type
CFAP20 p.Asp39Asn Uncertain significance ★ ⚠ same type
CFAP20 p.Gln92Arg Uncertain significance ★ ⚠ same type
CFAP20 p.Ile49Met Uncertain significance ★ ⚠ same type

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/cfap20-p-leu83val (accessed [today's date]).

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