Is AFAP1 p.Pro106Leu (c.317C>T) pathogenic?

AFAP1 p.Pro106Leu (c.317C>T) is classified Uncertain significance in AFAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-28). AlphaMissense: ambiguous (0.5421); Ultra-rare (popmax 0.0107%, nfe).

How common is AFAP1 p.Pro106Leu (c.317C>T) in the general population?

AFAP1 p.Pro106Leu (c.317C>T) is ultra-rare (popmax 0.0107%, nfe) (gnomAD).

What do computational predictors say about AFAP1 p.Pro106Leu (c.317C>T)?

AlphaMissense predicts ambiguous (score 0.5421) — an in-silico prediction, not a clinical call.

AFAP1 p.Pro106Leu

c.317C>T · rs368353828 · VCV2402626

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5421 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, nfe)

Computational evidence

Protein change
AlphaMissense	0.5421	ambiguous
REVEL	0.392	indeterminate
SaProt	LLR -7.38	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.5, phastCons 1
Regional constraint	o/e 1.14	unconstrained · MANE · 108 kb · p 3.6e-06 · regional, not allelic
Overall
CADD	32.0	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 0.0107% European (non-Finnish) · 126/1,178,166 alleles

Filtering AF 0.00912% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00856%

Overall 0.0085% 137/1,611,050 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0107%	9,351
African / African-American	0.00534%	18,715
Admixed American	0.00502%	19,924
Remaining individualsnot grpmax-eligible	0.00481%	20,787
East Asian	0.00223%	44,882

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: AFAP1
Protein: p.Pro106Leu
Coding: c.317C>T
MANE Select: NM_001134647
dbSNP: rs368353828
Type: single nucleotide variant
Location: chr4:7855483 (GRCh38)
Gene constraint: LOEUF 0.918 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.09

Full AFAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AFAP1 p.Val288Ala Uncertain significance ★★ ⚠ same type
AFAP1 p.Ala783= Likely benign ★★ same type
AFAP1 p.Asn686= Likely benign ★★ same type
AFAP1 p.Glu705= Benign ★★ same type
AFAP1 p.Ala438Ser Uncertain significance ★ ⚠ same type
AFAP1 p.Ala534Ser Uncertain significance ★ same type
AFAP1 p.Ala587Val Uncertain significance ★ same type
AFAP1 p.Ala624Val 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/afap1-p-pro106leu (accessed [today's date]).

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