Is AFMID p.Arg35Gln (c.104G>A) pathogenic?

AFMID p.Arg35Gln (c.104G>A) is classified Uncertain significance in AFMID (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-21). AlphaMissense: likely benign (0.1758); Ultra-rare (popmax 0.0358%, nfe).

How common is AFMID p.Arg35Gln (c.104G>A) in the general population?

AFMID p.Arg35Gln (c.104G>A) is ultra-rare (popmax 0.0358%, nfe) (gnomAD).

What do computational predictors say about AFMID p.Arg35Gln (c.104G>A)?

AlphaMissense predicts likely benign (score 0.1758) — an in-silico prediction, not a clinical call.

AFMID p.Arg35Gln

c.104G>A · rs138405849 · VCV2368771

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1758 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0358%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1758	likely benign
REVEL	0.111	moderately benign-leaning
SaProt	LLR -11.06	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP -0.71, phastCons 0.42
Regional constraint	o/e 0.97	unconstrained · MANE · 20 kb · p 0.53 · regional, not allelic
Overall
CADD	20.6	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 0.0358% European (non-Finnish) · 423/1,180,010 alleles

Filtering AF 0.033% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0319%

Overall 0.0283% 456/1,614,058 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0358%	2,790
African / African-American	0.0173%	5,773
Middle Eastern	0.0166%	6,040
Remaining individualsnot grpmax-eligible	0.0144%	6,944
Admixed American	0.00667%	14,998
South Asian	0.00659%	15,175

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: AFMID
Protein: p.Arg35Gln
Coding: c.104G>A
MANE Select: NM_001010982
dbSNP: rs138405849
Type: single nucleotide variant
Location: chr17:78191010 (GRCh38)
Gene constraint: LOEUF 1.018 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.39

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

Similar variants

AFMID p.Ala41Asp Uncertain significance ★ ⚠ same type
AFMID p.Arg238His Uncertain significance ★ ⚠ same type
AFMID p.Asn291Lys Uncertain significance ★ ⚠ same type
AFMID p.Asp247Asn Uncertain significance ★ ⚠ same type
AFMID p.Asp247Glu Uncertain significance ★ ⚠ same type
AFMID p.Asp247Val Uncertain significance ★ ⚠ same type
AFMID p.Cys237Gly Uncertain significance ★ ⚠ same type
AFMID p.Gln140Lys 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/afmid-p-arg35gln (accessed [today's date]).

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