Is CFAP418 c.243+20T>C pathogenic?

CFAP418 c.243+20T>C is classified Benign/Likely benign in CFAP418 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-01). Low-frequency (popmax 2.27%, afr); Associated with cone-rod dystrophy 16.

What condition is associated with CFAP418 c.243+20T>C?

CFAP418 c.243+20T>C is associated with cone-rod dystrophy 16, retinitis pigmentosa, bardet-biedl syndrome 21 (ClinVar).

How common is CFAP418 c.243+20T>C in the general population?

CFAP418 c.243+20T>C is low-frequency (popmax 2.27%, afr) (gnomAD).

How is Cone rod dystrophy inherited?

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

CFAP418 c.243+20T>C

rs10107484 · VCV1167428

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.27%, afr)

Conditions

cone-rod dystrophy 16

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +20	near-intronic (+20 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.61	GERP -2.5
Non-coding constraint	Z 1.00	1 kb window · o/e 0.92 · regional · uncalibrated
Overall
CADD	10.94	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.27% African / African-American · 1,631/71,790 alleles

Filtering AF 2.18% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.14%

Overall 0.125% 1,833/1,463,236 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.27%	44
Middle Eastern	0.161%	620
Remaining individualsnot grpmax-eligible	0.136%	736
Admixed American	0.128%	783
European (non-Finnish)	0.00354%	28,229
South Asian	0.00228%	43,817

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: CFAP418
Coding: c.243+20T>C
MANE Select: NM_177965
dbSNP: rs10107484
Type: single nucleotide variant
Location: chr8:95263667 (GRCh38)
Gene constraint: LOEUF 1.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.73

Full CFAP418 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cone-rod dystrophy 16 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: retinitis pigmentosa bardet-biedl syndrome 21

For Cone rod dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

CFAP418 p.Arg177Trp Pathogenic/Likely pathogenic ★★ same condition
CFAP418 p.Trp147Ter Pathogenic/Likely pathogenic ★★ same condition
CFAP418 c.*408G>A Uncertain significance ★★ same condition
CFAP418 c.*965C>G Uncertain significance ★★ same condition
CFAP418 p.Ala178Val Uncertain significance ★★ ⚠ same condition
CFAP418 p.Ala45Gly Uncertain significance ★★ ⚠ same condition
CFAP418 p.Arg177Gln Uncertain significance ★★ ⚠ same condition
CFAP418 p.Arg186Gly 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/cfap418-c-243-plus-20t-c (accessed [today's date]).

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