Is ROR1 p.Arg6Ser (c.16C>A) pathogenic?

ROR1 p.Arg6Ser (c.16C>A) is classified Uncertain significance in ROR1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-08). AlphaMissense: likely benign (0.2279); Ultra-rare (popmax 0.0162%, afr).

How common is ROR1 p.Arg6Ser (c.16C>A) in the general population?

ROR1 p.Arg6Ser (c.16C>A) is ultra-rare (popmax 0.0162%, afr) (gnomAD).

What do computational predictors say about ROR1 p.Arg6Ser (c.16C>A)?

AlphaMissense predicts likely benign (score 0.2279) — an in-silico prediction, not a clinical call.

ROR1 p.Arg6Ser

c.16C>A · rs1205371508 · VCV2964495

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2279 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0162%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2279	likely benign
REVEL	0.056	moderately benign-leaning
SaProt	LLR -7.58	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 0.43	GERP -1.6, phastCons 0.99
Regional constraint	o/e 1.10	unconstrained · MANE · 235 kb · p 0.43 · regional, not allelic
Overall
CADD	18.47	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0162% African / African-American · 10/61,708 alleles

Filtering AF 0.00877% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00664%

Overall 0.00102% 12/1,176,020 alleles · ultra-rare exomes 3/1,026,390 · genomes 9/149,630 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0162%	6,171
Admixed American	0.00473%	21,164
Remaining individualsnot grpmax-eligible	0.00244%	41,000

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: ROR1
Protein: p.Arg6Ser
Coding: c.16C>A
MANE Select: NM_005012
dbSNP: rs1205371508
Type: single nucleotide variant
Location: chr1:63774433 (GRCh38)
Gene constraint: LOEUF 0.326 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.17 · 5 PDB

Full ROR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ROR1 p.Ala596Ser Uncertain significance ★★ ⚠ same type
ROR1 p.Ala833Ser Uncertain significance ★★ ⚠ same type
ROR1 p.Ala923Gly Uncertain significance ★★ ⚠ same type
ROR1 p.Ala923Thr Uncertain significance ★★ ⚠ same type
ROR1 p.Ala935Val Uncertain significance ★★ ⚠ same type
ROR1 p.Arg25His Uncertain significance ★★ ⚠ same type
ROR1 p.Arg429Gln Uncertain significance ★★ same type
ROR1 p.Arg474Cys 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/ror1-p-arg6ser (accessed [today's date]).

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