Is CFAP52 p.Ser312= (c.936G>A) pathogenic?

CFAP52 p.Ser312= (c.936G>A) is classified Likely benign in CFAP52 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-18). Ultra-rare (popmax 0.0921%, nfe); Associated with situs inversus.

What condition is associated with CFAP52 p.Ser312= (c.936G>A)?

CFAP52 p.Ser312= (c.936G>A) is associated with situs inversus (ClinVar).

How common is CFAP52 p.Ser312= (c.936G>A) in the general population?

CFAP52 p.Ser312= (c.936G>A) is ultra-rare (popmax 0.0921%, nfe) (gnomAD).

CFAP52 p.Ser312=

c.936G>A · rs146057434 · VCV1092021

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0921%, nfe)

Conditions

situs inversus

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 -2.4	GERP -3.8
Overall
CADD	5.611	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0921% European (non-Finnish) · 1,087/1,180,036 alleles

Filtering AF 0.0875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0857%

Overall 0.0709% 1,144/1,614,162 alleles · ultra-rare exomes 1,057/1,461,860 · genomes 87/152,302 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0921%	1,086
Remaining individualsnot grpmax-eligible	0.04%	2,500
Admixed American	0.0183%	5,457
Finnishnot grpmax-eligible	0.0172%	5,820
African / African-American	0.012%	8,338
South Asian	0.0011%	91,080

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: CFAP52
Protein: p.Ser312=
Coding: c.936G>A
MANE Select: NM_145054
dbSNP: rs146057434
Type: single nucleotide variant
Location: chr17:9612390 (GRCh38)
Gene constraint: LOEUF 1.022 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.59 · 2 PDB

Full CFAP52 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

situs inversus — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CFAP52 p.Ala147Thr Uncertain significance ★★ ⚠ same condition
CFAP52 p.Ala161Asp Uncertain significance ★★ ⚠ same condition
CFAP52 p.Arg170Gln Uncertain significance ★★ ⚠ same condition
CFAP52 p.Arg594Cys Uncertain significance ★★ ⚠ same condition
CFAP52 p.Gly343Ser Uncertain significance ★★ ⚠ same condition
CFAP52 p.Gly534Ala Uncertain significance ★★ same condition
CFAP52 p.Met551Thr Uncertain significance ★★ ⚠ same condition
CFAP52 p.Tyr41His 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/cfap52-p-ser312 (accessed [today's date]).

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