Is SCRIB p.Arg1116His (c.3347G>A) pathogenic?

SCRIB p.Arg1116His (c.3347G>A) is classified Uncertain significance in SCRIB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-30). AlphaMissense: ambiguous (0.3989); Very rare (popmax 0.00802%, afr).

How common is SCRIB p.Arg1116His (c.3347G>A) in the general population?

SCRIB p.Arg1116His (c.3347G>A) is very rare (popmax 0.00802%, afr) (gnomAD).

What do computational predictors say about SCRIB p.Arg1116His (c.3347G>A)?

AlphaMissense predicts ambiguous (score 0.3989) — an in-silico prediction, not a clinical call.

SCRIB p.Arg1116His

c.3347G>A · VCV3951091

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3989 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00802%, afr)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.3989	ambiguous
REVEL	0.262	benign-leaning
SaProt	LLR -10.23	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.5, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 20 kb · p 9.1e-08 · regional, not allelic
Overall
CADD	27.0	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 0.00802% African / African-American · 6/74,770 alleles

Filtering AF 0.00348% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.000692% 11/1,590,450 alleles · very rare exomes 7/1,438,396 · genomes 4/152,054 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00802%	12,462
East Asian	0.00226%	44,328
South Asian	0.00112%	89,112
European (non-Finnish)	0.000255%	391,495

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: SCRIB
Protein: p.Arg1116His
Coding: c.3347G>A
MANE Select: NM_182706
Type: single nucleotide variant
Location: chr8:143803714 (GRCh38)
Gene constraint: LOEUF 0.684 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.33 · 42 PDB
Residue 1116: a β-strand; the pdz 4 domain; the 'interaction with arhgef7' region; the 'required for interaction with vim' region; the 'interaction with tick-borne encephalitis virus rna-directed rna polymerase ns5' region

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

Similar variants

SCRIB c.3120+10C>G Benign/Likely benign ★★ same type
SCRIB c.504-9C>T Benign ★★ same type
SCRIB p.Ala1488= Likely benign ★★ same type
SCRIB p.Arg492= Benign ★★ same type
SCRIB p.Asn647= Benign/Likely benign ★★ same type
SCRIB p.Leu254= Benign ★★ same type
SCRIB p.Phe571= Benign ★★ same type
SCRIB p.Pro1343= 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/scrib-p-arg1116his (accessed [today's date]).

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