Is DBR1 p.Asn364Ser (c.1091A>G) pathogenic?

DBR1 p.Asn364Ser (c.1091A>G) is classified Benign in DBR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-22). AlphaMissense: likely benign (0.0515); Low-frequency (popmax 2.94%, eas).

How common is DBR1 p.Asn364Ser (c.1091A>G) in the general population?

DBR1 p.Asn364Ser (c.1091A>G) is low-frequency (popmax 2.94%, eas) (gnomAD).

What do computational predictors say about DBR1 p.Asn364Ser (c.1091A>G)?

AlphaMissense predicts likely benign (score 0.0515) — an in-silico prediction, not a clinical call.

DBR1 p.Asn364Ser

c.1091A>G · rs117574050 · VCV2040593

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0515 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.94%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0515	likely benign
REVEL	0.346	indeterminate
SaProt	LLR -9.98	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -12
Regional constraint	o/e 0.30	constrained · MANE · 56 bp · p 0.00064 · regional, not allelic
Overall
CADD	0.044	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 2.94% East Asian · 1,318/44,866 alleles

Filtering AF 2.81% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.75%

Overall 0.103% 1,658/1,614,166 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	2.94%	34
Remaining individualsnot grpmax-eligible	0.144%	694
African / African-American	0.128%	782
Ashkenazi Jewishnot grpmax-eligible	0.101%	987
South Asian	0.079%	1,265
Admixed American	0.01%	10,003
European (non-Finnish)	0.0039%	25,653

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: DBR1
Protein: p.Asn364Ser
Coding: c.1091A>G
MANE Select: NM_016216
dbSNP: rs117574050
Type: single nucleotide variant
Location: chr3:138162433 (GRCh38)
Gene constraint: LOEUF 0.841 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.04
Residue 364: a UniProt-annotated variant site (in iiae11; loss of protein expression)

Full DBR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DBR1 c.489+5G>A Uncertain significance ★★ same type
DBR1 p.Ala233Thr Uncertain significance ★★ ⚠ same type
DBR1 p.Ala443Thr Uncertain significance ★★ ⚠ same type
DBR1 p.Ala458Asp Uncertain significance ★★ ⚠ same type
DBR1 p.Arg197Gln Uncertain significance ★★ ⚠ same type
DBR1 p.Arg197Ter Uncertain significance ★★ same type
DBR1 p.Arg527Ser Uncertain significance ★★ ⚠ same type
DBR1 p.Asn405His 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/dbr1-p-asn364ser (accessed [today's date]).

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