Is DDR2 p.Ser677= (c.2031C>T) pathogenic?

DDR2 p.Ser677= (c.2031C>T) is classified Conflicting classifications of pathogenicity in DDR2 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-11-11). Ultra-rare (popmax 0.0329%, mid); Associated with spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome.

How common is DDR2 p.Ser677= (c.2031C>T) in the general population?

DDR2 p.Ser677= (c.2031C>T) is ultra-rare (popmax 0.0329%, mid) (gnomAD).

DDR2 p.Ser677=

Q: What condition is associated with DDR2 p.Ser677= (c.2031C>T)?

DDR2 p.Ser677= (c.2031C>T) is associated with spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome (ClinVar).

Q: How is Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.2031C>T · rs773962213 · VCV719940

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0329%, mid)

Conditions

spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome

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 0.5	GERP -0.014, phastCons 0.25
Overall
CADD	10.78	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0329% Middle Eastern · 2/6,084 alleles

Filtering AF 0.009% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00681%

Overall 0.00143% 23/1,613,864 alleles · ultra-rare exomes 22/1,461,756 · genomes 1/152,108 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0329%	3,042
Admixed American	0.0167%	5,999
South Asian	0.00329%	30,361
Remaining individualsnot grpmax-eligible	0.0032%	31,241
European (non-Finnish)	0.000508%	196,663

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: DDR2
Protein: p.Ser677=
Coding: c.2031C>T
MANE Select: NM_006182
dbSNP: rs773962213
Type: single nucleotide variant
Location: chr1:162775826 (GRCh38)
Gene constraint: LOEUF 0.375 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.57 · 5 PDB
Residue 677: the protein kinase domain

Full DDR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

DDR2 p.Arg752Cys Likely pathogenic ★★ same condition
DDR2 c.-27-11G>C Uncertain significance ★★ same condition
DDR2 c.*48A>G Uncertain significance ★★ same condition
DDR2 p.Arg128His Uncertain significance ★★ ⚠ same condition
DDR2 p.Arg165Gln Uncertain significance ★★ ⚠ same condition
DDR2 p.Arg260Trp Uncertain significance ★★ ⚠ same condition
DDR2 p.Arg307Cys Uncertain significance ★★ ⚠ same condition
DDR2 p.Arg668His Uncertain significance ★★ ⚠ 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/ddr2-p-ser677 (accessed [today's date]).

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