Is CFAP70 p.Pro320Leu (c.959C>T) pathogenic?

CFAP70 p.Pro320Leu (c.959C>T) is classified Likely benign in CFAP70 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-01). AlphaMissense: likely benign (0.0858); Rare (popmax 0.85%, afr).

How common is CFAP70 p.Pro320Leu (c.959C>T) in the general population?

CFAP70 p.Pro320Leu (c.959C>T) is rare (popmax 0.85%, afr) (gnomAD).

What do computational predictors say about CFAP70 p.Pro320Leu (c.959C>T)?

AlphaMissense predicts likely benign (score 0.0858) — an in-silico prediction, not a clinical call.

CFAP70 p.Pro320Leu

c.959C>T · VCV4820910

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0858 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.85%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0858	likely benign
REVEL	0.038	moderately benign-leaning
SaProt	LLR -8.29	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.5	GERP 1.8, phastCons 1
Overall
CADD	18.49	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 0.85% African / African-American · 637/74,936 alleles

Filtering AF 0.795% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.774%

Overall 0.049% 791/1,612,846 alleles · rare exomes 410/1,460,740 · genomes 381/152,106 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.85%	118
Middle Eastern	0.0991%	1,009
Remaining individualsnot grpmax-eligible	0.0913%	1,096
Admixed American	0.0835%	1,198
European (non-Finnish)	0.00331%	30,240
South Asian	0.0022%	45,431

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: CFAP70
Protein: p.Pro320Leu
Coding: c.959C>T
MANE Select: NM_001367801
Type: single nucleotide variant
Location: chr10:73331205 (GRCh38)
Gene constraint: LOEUF 0.75 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.55

Full CFAP70 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP70 p.His372Tyr Likely benign ★★ same type
CFAP70 p.Ala433Pro Uncertain significance ★ ⚠ same type
CFAP70 p.Ala759Glu Uncertain significance ★ ⚠ same type
CFAP70 p.Ala78Thr Uncertain significance ★ ⚠ same type
CFAP70 p.Ala7Pro Uncertain significance ★ ⚠ same type
CFAP70 p.Ala948Val Uncertain significance ★ ⚠ same type
CFAP70 p.Ala955Ser Uncertain significance ★ ⚠ same type
CFAP70 p.Arg1045Trp 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/cfap70-p-pro320leu (accessed [today's date]).

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