Is CFAP65 p.Thr320= (c.960G>A) pathogenic?

CFAP65 p.Thr320= (c.960G>A) is classified Likely benign in CFAP65 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-01). Rare (popmax 0.114%, nfe).

How common is CFAP65 p.Thr320= (c.960G>A) in the general population?

CFAP65 p.Thr320= (c.960G>A) is rare (popmax 0.114%, nfe) (gnomAD).

CFAP65 p.Thr320=

c.960G>A · rs150728769 · VCV2651910

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.114%, nfe)

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 -10	GERP -3.7
Overall
CADD	1.183	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.114% European (non-Finnish) · 1,348/1,178,108 alleles

Filtering AF 0.109% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.107%

Overall 0.096% 1,545/1,609,338 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.132%	756
European (non-Finnish)grpmax	0.114%	874
Remaining individualsnot grpmax-eligible	0.0931%	1,074
Ashkenazi Jewishnot grpmax-eligible	0.0578%	1,730
Admixed American	0.0388%	2,578
African / African-American	0.016%	6,253
East Asian	0.00447%	22,377
South Asian	0.00111%	89,960

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CFAP65
Protein: p.Thr320=
Coding: c.960G>A
MANE Select: NM_194302
dbSNP: rs150728769
Type: single nucleotide variant
Location: chr2:219031161 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.03

Full CFAP65 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP65 p.Arg1231= Benign ★★ same type
CFAP65 p.Arg1545Gln Benign ★★ same type
CFAP65 p.Arg760Gln Benign ★★ same type
CFAP65 p.Asp1313= Likely benign ★★ same type
CFAP65 p.Leu1127= Benign/Likely benign ★★ same type
CFAP65 p.Leu1523= Benign/Likely benign ★★ same type
CFAP65 p.Leu1906= Benign/Likely benign ★★ same type
CFAP65 p.Lys1805= Likely benign ★★ 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/cfap65-p-thr320 (accessed [today's date]).

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