Is SYNCRIP p.Gln592= (c.1776G>A) pathogenic?

SYNCRIP p.Gln592= (c.1776G>A) is classified Likely benign in SYNCRIP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-28). Ultra-rare (popmax 0.0308%, nfe); Associated with SYNCRIP-related disorder.

What condition is associated with SYNCRIP p.Gln592= (c.1776G>A)?

SYNCRIP p.Gln592= (c.1776G>A) is associated with SYNCRIP-related disorder (ClinVar).

How common is SYNCRIP p.Gln592= (c.1776G>A) in the general population?

SYNCRIP p.Gln592= (c.1776G>A) is ultra-rare (popmax 0.0308%, nfe) (gnomAD).

SYNCRIP p.Gln592=

c.1776G>A · rs199509715 · VCV3046652

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0308%, nfe)

Conditions

SYNCRIP-related disorder

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 7.7	GERP 2.2, phastCons 1
Overall
CADD	11.69	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0308% European (non-Finnish) · 363/1,180,040 alleles

Filtering AF 0.0281% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0271%

Overall 0.0234% 377/1,614,048 alleles · ultra-rare exomes 360/1,461,886 · genomes 17/152,162 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0308%	3,251
Remaining individualsnot grpmax-eligible	0.016%	6,249
African / African-American	0.00534%	18,728

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: SYNCRIP
Protein: p.Gln592=
Coding: c.1776G>A
MANE Select: NM_006372
dbSNP: rs199509715
Type: single nucleotide variant
Location: chr6:85614852 (GRCh38)
Gene constraint: LOEUF 0.249 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 70.83 · 4 PDB
Residue 592: the 'disordered' region

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

Disease context

SYNCRIP-related disorder

Similar variants

SYNCRIP p.Ala521Thr Uncertain significance ★ ⚠ same condition
SYNCRIP p.Trp622Arg Uncertain significance ★ ⚠ same condition
SYNCRIP p.Val561Gly Uncertain significance ★ ⚠ same condition
SYNCRIP p.Thr101Ile Uncertain significance ⚠ same condition
SYNCRIP p.Tyr523His Uncertain significance ⚠ same condition
SYNCRIP p.Arg548= Likely benign same condition
SYNCRIP p.Gln596= Likely benign same condition
SYNCRIP p.Pro147fs Likely pathogenic ★ 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/syncrip-p-gln592 (accessed [today's date]).

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