Is AFAP1L2 p.Ala74Val (c.221C>T) pathogenic?

AFAP1L2 p.Ala74Val (c.221C>T) is classified Likely benign in AFAP1L2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-09). AlphaMissense: likely benign (0.0589); Very rare (popmax 0.00397%, amr).

How common is AFAP1L2 p.Ala74Val (c.221C>T) in the general population?

AFAP1L2 p.Ala74Val (c.221C>T) is very rare (popmax 0.00397%, amr) (gnomAD).

What do computational predictors say about AFAP1L2 p.Ala74Val (c.221C>T)?

AlphaMissense predicts likely benign (score 0.0589) — an in-silico prediction, not a clinical call.

AFAP1L2 p.Ala74Val

c.221C>T · VCV4247336

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0589 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00397%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0589	likely benign
REVEL	0.02	moderately benign-leaning
SaProt	LLR -6.63	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 -3.8	GERP -3.7
Regional constraint	o/e 0.81	unconstrained · MANE · 100 kb · p 3.6e-05 · regional, not allelic
Overall
CADD	0.114	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 0.00397% Admixed American · 1/25,162 alleles

Filtering AF 0.000144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000105%

Overall 0.000615% 8/1,300,052 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00397%	25,162
East Asian	0.00311%	32,204
African / African-American	0.00154%	64,992
European (non-Finnish)	0.000493%	202,995

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: AFAP1L2
Protein: p.Ala74Val
Coding: c.221C>T
MANE Select: NM_001001936
Type: single nucleotide variant
Location: chr10:114331897 (GRCh38)
Gene constraint: LOEUF 0.605 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.56 · 1 PDB
Residue 74: the 'disordered' region

Full AFAP1L2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AFAP1L2 p.Arg648His Uncertain significance ★★ ⚠ same type
AFAP1L2 p.Arg730= Benign/Likely benign ★★ same type
VWA2 p.Arg682Trp Benign ★★ ⚠ same type
VWA2 p.Asn331= Benign ★★ same type
VWA2 p.Gly641= Likely benign ★★ same type
VWA2 p.His496Tyr Benign ★★ same type
VWA2 p.Phe365= Benign ★★ same type
VWA2 p.Pro544= 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/afap1l2-p-ala74val (accessed [today's date]).

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