Is DCBLD2 p.Ile672Val (c.2014A>G) pathogenic?

DCBLD2 p.Ile672Val (c.2014A>G) is classified Likely benign in DCBLD2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-02-25). AlphaMissense: likely benign (0.0549); Rare (popmax 0.589%, nfe); Associated with DCBLD2-related disorder.

What condition is associated with DCBLD2 p.Ile672Val (c.2014A>G)?

DCBLD2 p.Ile672Val (c.2014A>G) is associated with DCBLD2-related disorder (ClinVar).

How common is DCBLD2 p.Ile672Val (c.2014A>G) in the general population?

DCBLD2 p.Ile672Val (c.2014A>G) is rare (popmax 0.589%, nfe) (gnomAD).

What do computational predictors say about DCBLD2 p.Ile672Val (c.2014A>G)?

AlphaMissense predicts likely benign (score 0.0549) — an in-silico prediction, not a clinical call.

DCBLD2 p.Ile672Val

c.2014A>G · rs111245657 · VCV3060115

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0549 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.589%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

DCBLD2-related disorder

Computational evidence

Protein change
AlphaMissense	0.0549	likely benign
REVEL	0.006	strongly benign-leaning
SaProt	LLR -5.07	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 -0.073	GERP -4.5, phastCons 0.001
Regional constraint	o/e 0.89	unconstrained · MANE · 23 kb · p 0.0054 · regional, not allelic
Overall
CADD	0.154	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 0.589% European (non-Finnish) · 6,950/1,179,876 alleles

Filtering AF 0.577% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.573%

Overall 0.466% 7,517/1,613,996 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.589%	170
Remaining individualsnot grpmax-eligible	0.365%	274
Admixed American	0.242%	414
Finnishnot grpmax-eligible	0.161%	622
African / African-American	0.108%	926
Ashkenazi Jewishnot grpmax-eligible	0.0236%	4,230
Middle Eastern	0.0165%	6,062
South Asian	0.0022%	45,543

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: DCBLD2
Protein: p.Ile672Val
Coding: c.2014A>G
MANE Select: NM_080927
dbSNP: rs111245657
Type: single nucleotide variant
Location: chr3:98799686 (GRCh38)
Gene constraint: LOEUF 0.808 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.13

Full DCBLD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DCBLD2-related disorder

Similar variants

DCBLD2 p.Asp388Asn Likely benign ⚠ same condition
DCBLD2 p.Lys391= Benign ★★ same type
DCBLD2 p.Ala182Thr Uncertain significance ★ ⚠ same type
DCBLD2 p.Ala24Ser Uncertain significance ★ ⚠ same type
DCBLD2 p.Ala304Glu Uncertain significance ★ ⚠ same type
DCBLD2 p.Ala304Thr Uncertain significance ★ ⚠ same type
DCBLD2 p.Ala304Val Uncertain significance ★ ⚠ same type
DCBLD2 p.Ala341Thr 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/dcbld2-p-ile672val (accessed [today's date]).

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